Cambridge International As and A Level Biology Students Book 2nd Edition (C. J. Clegg, Geoff G..

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Cambridge
International AS & A Level
Biology
Second edition
CJ Clegg
482876_FM_Biology_i-x.indd 1 20/02/20 11:52 AM

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ISBN: 9781510482876

Contents
Introduction vi
AS LEVEL
1 Cell structure
1.1 The microscope in cell studies 1
1.2 Cells as the basic units of living organisms 13
2 Biological molecules
2.1 Testing for biological molecules 31
2.2 Carbohydrates and lipids 35
2.3 Proteins 47
2.4 Water 55
3 Enzymes
3.1 Mode of action of enzymes 61
3.2 Factors that affect enzyme action 69
4 Cell membranes and transport

4.1 Fluid mosaic membranes 81
4.2 Movement into and out of cells 86
5 The mitotic cell cycle

5.1 Replication and division of nuclei and cells 106
5.2 Chromosome behaviour in mitosis 115
6 Nucleic acids and protein synthesis

6.1 Structure of nucleic acids and replication of DNA 120
6.2 Protein synthesis 129
7 Transport in plants
7.1 Structure of transport tissues 142
7.2 Transport mechanisms 149
8 Transport in mammals
8.1 The circulatory system 166
8.2 Transport of oxygen and carbon dioxide 176
8.3 The heart 179
iii

9 Gas exchange
Contents
9.1 The gas exchange system 188
10 Infectious diseases
10.1 Infectious diseases 200
10.2 Antibiotics 216
11 Immunity
11.1 The immune system 224
11.2 Antibodies and vaccination 231
A LEVEL
12 Energy and respiration

12.1 Energy 240
12.2 Respiration 248
13 Photosynthesis
13.1 Photosynthesis as an energy transfer process 269
13.2 Investigation of limiting factors 282
14 Homeostasis
14.1 Homeostasis in mammals 291
14.2 Homeostasis in plants 312
15 Control and coordination

15.1 Control and coordination in mammals 317
15.2 Control and coordination in plants 335
16 Inheritance
16.1 Passage of information from parents to offspring 343
16.2 The roles of genes in determining the phenotype 350
16.3 Gene control 373
17 Selection and evolution

17.1 Variation 380
17.2 Natural and artificial selection 386
17.3 Evolution 401
18 Classification, biodiversity and conservation

18.1 Classification 415
18.2 Biodiversity 426
18.3 Conservation 439
iv

19 Genetic technology
Contents
19.1 Principles of genetic technology 458
19.2 Genetic technology applied to medicine 472
19.3 Genetically modified organisms in agriculture 482
Answers 488
Glossary 521
Index 524
Acknowledgements 533

Introduction
Welcome to the second edition of Cambridge International AS & A Level Biology. This
textbook has been revised to comprehensively cover the Cambridge International AS &
A Level Biology syllabus (9700) for first examination from 2022.
This textbook is part of a suite of resources, which also includes a Practical Skills
Workbook, Online Teacher’s Resources and a Study and Revision Guide.
How to use this book

This textbook, endorsed by Cambridge Assessment International Education, has been
designed to make your study of biology as successful and rewarding as possible.
Organisation
The book is divided into two parts. Topics 1–11 cover the AS Level syllabus content and
Topics 12–19 cover the content required by students studying the full A Level course.
The titles of the topics in the book match those in the syllabus exactly. In almost all
cases, the subheadings within topics also match those in the syllabus.
Answers to questions are included at the back of the book.
Features
Each topic contains a number of features designed to help you navigate the syllabus
content effectively.
At the start of each topic, there is a blue box that provides a summary of the syllabus
points to be covered in that topic. These are the exact Learning outcomes listed in the
syllabus.
Learning outcomes
By the end of this topic, you will be able to:
1.1.1 make temporary preparations of cellular material suitable for viewing
with a light microscope
1.1.2 draw cells from microscope slides and photomicrographs
1.1.3 calculate magnifications of images and actual sizes of specimens from
drawings, photomicrographs and electron micrographs (scanning and
transmission)
1.1.4 use an eyepiece graticule and stage micrometer scale to make
measurements and use the appropriate units, millimetre (mm),
micrometre (μm) and nanometre (nm)
1.1.5 define resolution and magnification and explain the differences between
these terms, with reference to light microscopy and electron microscopy
Each topic also has a number of Starting points, key bits of information that it may be
useful to remind yourself of before you begin to read.
Starting point
★ An understanding of the principles of microscopy shows why light and
electron microscopes have been essential in improving our knowledge of
cells.
vi

Question exercises give you opportunities to test your understanding of the topic.
Introduction
Question 1 State the essential processes characteristic of living things.
Material that goes beyond the requirements of the Cambridge International AS & A
Level syllabus, but which may be of interest, especially to those of you planning to study
Biology at a higher level, is clearly labelled in Extension boxes.
EXTENSION
Alternatively, images of cells and tissues viewed may be further magnified,
displayed or projected (and saved for printing out) by the technique of digital
microscopy. A digital microscope is used, or an appropriate video camera is
connected by a microscope coupler or eyepiece adaptor that replaces the standard
microscope eyepiece. Images are displayed via video recorder, TV monitor or
computer.
At the end of each topic, there is a Summary of the key points that have been covered.
SUMMARY
» Cells are the building blocks of living things. and they have a true nucleus. These living things 1
They are derived from other cells by division and are called eukaryotes.
they are the site of all the chemical reactions of » Examination of transmission electron
life (metabolism). A cell is the smallest unit of micrographs has revealed that the cytoplasm of
organisation we can say is alive. the eukaryotic cell contains numerous organelles,
» Cells are extremely small. They are measured in some about the size of bacteria, suspended in an
units of a thousandths of a millimetre (a micron – aquatic solution of metabolites (called the cytosol)
End of chapter questions

µm) and they must be viewed by microscopy. In the surrounded by the cell surface membrane.
laboratory we view them by light microscopy using » Many of the organelles are membrane-bound
a compound microscope. structures, including the nucleus, mitochondria,
» The cells of plants and animals have common chloroplasts, endoplasmic reticulum, Golgi
features, including a nucleus, cytoplasm and apparatus and lysosomes. The organelles have
cell membrane. To observe and resolve the specific roles in metabolism. The biochemical
detailed structures within the cytoplasm, roles of the organelles are investigated by
electron microscopy is required. The distinctive disrupting cells and isolating the organelles for
features of plant cells are a cellulose cell wall, further investigation.
the presence of large permanent vacuoles and » Viruses are non-cellular structures that consist of
the possible presence of chloroplasts, the site of a core of nucleic acid (DNA or RNA) surrounded by
photosynthesis. a protein coat, called a capsid. They are extremely
» The simplest cellular organisation is shown by small when compared with bacteria, and they
bacteria. Here there is no true nucleus. These can reproduce only inside specific living cells, so
unicellular organisms are called prokaryotes. viruses function as endoparasites in their host
The cells of plants, animals and fungi are larger organism.
END OF CHAPTER QUESTIONS

1 a Place the following organelles in order of size, starting with the smallest:
lysosome mitochondria nucleus ribosome [2]
b What is the most likely role of the pores in the nuclear envelope (membrane),
given that the nucleus controls and directs the activities of the cell? [1]
c i Where in the cell are the ribosomes found? [2]
ii How does the function of ribosomes vary according to where they occur? [2]
d Which cell structures synthesise and transport lipids in the cell? [3]
e Which of the organelles of the cell are surrounded by a double membrane? [3] vii
f i What is the origin of the cristae within the mitochondria? [1]
ii What is the value of the surface area the cristae provide? [2]
g Name a cell in which you would expect to find a large number of
482876_FM_Biology_i-x.indd 7
lysosomes and say why. [4]20/02/20 11:52 AM
Finally, each topic ends with a set of End of topic questions; some are exam-style questions
Introduction
written by the author, others are taken from Cambridge International AS & A Level Biology
(9700) past examination papers. Both of these have marks allocated per question part.
There are also some questions that test knowledge recall and have no marks allocated.
END OF TOPIC QUESTIONS

e Which of the organelles of the cell are surrounded by a double membrane? [3]
lysosomes and say why. [4]
[Total: 20]
Assessment
If you are following the Cambridge International AS Level course, you will take three
examination papers:
» Paper 1 Multiple Choice (1 hour 15 minutes)
» Paper 2 AS Level Structured Questions (1 hour 15 minutes)
» Paper 3 Advanced Practical Skills (2 hours)
If you are studying the Cambridge International A Level course, you will take five
examination papers. These are Papers 1, 2 and 3, and also:
» Paper 4 A Level Structured Questions (2 hours)
» Paper 5 Planning, Analysis and Evaluation (1 hour 15 minutes)
The information in this section is based on the 9700 syllabus for examination from
2022. You should always refer to the appropriate syllabus document for the year of your
examination to confirm the details and for more information. The syllabus document is
available on the Cambridge International website at www.cambridgeinternational.org.
viii

Command words
Introduction
The table below, taken from the syllabus, includes command words used in the
assessment for this syllabus. The use of the command word will relate to the subject
context. Make sure you are familiar with these.
Command word What it means

Assess Make an informed judgement
Calculate Work out from given facts, figures or information
Comment Give an informed opinion
Compare Identify/comment on similarities and/or differences
Contrast Identify/comment on differences
Define Give precise meaning
Describe State the points of a topic/give characteristics and main features
Discuss Write about issue(s) or topic(s) in depth in a structured way
Explain Set out purposes or reasons/make the relationships between things
evident/provide why and/or how and support with relevant evidence
Give Produce an answer from a given source or recall/memory
Identify Name/select/recognise
Outline Set out main points
Predict Suggest what may happen based on available information
Sketch Make a simple drawing showing the key features
State Express in clear terms
Suggest Apply knowledge and understanding to situations where there are
a range of valid responses in order to make proposals/put forward
considerations
Notes for teachers

Key concepts
These are the essential ideas that help learners to develop a deep understanding of the
subject and to make links between the different topics. Although teachers are likely to
have these in mind at all times when they are teaching the syllabus, the following icons are
included in the textbook at points where the key concepts particularly relate to the text.
Cells as the units of life
A cell is the basic unit of life and all organisms are composed of one or more cells. There
are two fundamental types of cell: prokaryotic and eukaryotic. Understanding how cells
work provides an insight into the fundamental processes of all living organisms.
Biochemical processes
Cells are dynamic structures within which the chemistry of life takes place. Biochemistry
and molecular biology help to explain how and why cells function as they do.
DNA, the molecule of heredity
Cells contain the molecule of heredity, DNA. DNA is essential for the continuity and
evolution of life by allowing genetic information to be stored accurately, to be copied
to daughter cells, to be passed from one generation to the next and for the controlled
production of proteins. Rare errors in the accurate copying of DNA, known as mutations,
result in genetic variation and are essential for evolution.
ix

Natural selection
Introduction
Natural selection acts on genetic variation and is the major mechanism in evolution,
including speciation. Natural selection results in the accumulation of beneficial genetic
mutations within populations and explains how populations can adapt to meet the
demands of changing environments.
Organisms in their environment
All organisms interact with their biotic and abiotic environment. Studying these
interactions allows biologists to understand better the effect of human activities on
ecosystems, to develop more effective strategies to conserve biodiversity and to predict
more accurately the future implications for humans of changes in the natural world.
Observation and experiment
The different fields of biology are intertwined and cannot be studied in isolation.
Observation, enquiry, experimentation and fieldwork are fundamental to biology,
allowing relevant evidence to be collected and considered as a basis on which to
build new models and theories. Such models and theories are further tested by
experimentation and observation in a cyclical process of feedback and refinement,
allowing the development of robust and evidence-based conceptual understandings.
Additional support
A number of other Hodder Education resources are available to help teachers deliver the
Cambridge International AS & A Level Biology syllabus.
» The Cambridge International AS & A Level Biology Practical Skills Workbook is a write-
in resource designed to be used throughout the course and provides students extra
opportunities to test their understanding of the practical skills required by the
syllabus.
» The Cambridge International AS & A Level Biology Online Teacher’s Resources include
an introduction to teaching the course, a scheme of work and additional teaching
resources.
» The Cambridge International AS & A Level Biology Study and Revision Guide is a stand-
alone resource that is designed to be used independently by students at the end of
their course of study as they prepare for their examinations. This title has not been
through the Cambridge International endorsement process.
Author’s acknowledgements
I am indebted to the experienced international teachers and the students who I have
been privileged to meet in Asia and in the UK in the process of preparing this material.
I am especially indebted to Christine Lea, an experienced teacher and examiner of
Biology who has guided me topic by topic on the special needs of the students for whom
this book is designed. I would also like to thank Salma Siddiqui who provided the new
content required to bring this book in line with the revised syllabus.
Finally, I am indebted to the publishing team at Hodder Education, freelance
development editor Michala Green and freelance project editor Sophie Clark whose skill
and patience have brought together text and illustration as I have wished. I am most
grateful to them.
Dr Chris Clegg
Salisbury, Wiltshire, UK
March, 2020

AS LEVEL
1 Cell structure
1.1 The microscope in cell studies

All organisms are composed Learning outcomes
of cells. Knowledge of the
structure and function of By the end of this topic, you will be able to:
cells underpins much of 1.1.1 make temporary preparations of cellular material suitable for viewing
biology. The fundamental with a light microscope
differences between 1.1.2 draw cells from microscope slides and photomicrographs
eukaryotic and prokaryotic
1.1.3 calculate magnifications of images and actual sizes of specimens from
cells are explored and
drawings, photomicrographs and electron micrographs (scanning and
provide useful biological
background for Topic 10 transmission)
Infectious diseases. 1.1.4 use an eyepiece graticule and stage micrometer scale to make
Viruses are introduced as measurements and use the appropriate units, millimetre (mm),
non-cellular structures, micrometre (μm) and nanometre (nm)
which gives students the 1.1.5 define resolution and magnification and explain the differences between
opportunity to consider these terms, with reference to light microscopy and electron microscopy
whether cells are a
fundamental property of life.
The use of light microscopes Starting point
is a fundamental skill that
is developed in this topic ★ An understanding of the principles of microscopy shows why light and
and applied throughout electron microscopes have been essential in improving our knowledge of
several other sections of the cells.
syllabus.

Introducing cells
The cell is the basic unit of living matter – the smallest part of an organism which we
can say is alive. It is cells that carry out the essential processes of life. We think of them
as self-contained units of structure and function. Some organisms are made of a single
cell and are known as unicellular. Examples of unicellular organisms are introduced in
Figure 1.1 on the next page. In fact, there are vast numbers of different unicellular
organisms in the living world, many with a very long evolutionary history.
Other organisms are made of many cells and are known as multicellular organisms.
Examples of multicellular organisms are the mammals and flowering plants. Much of
the biology in this book is about multicellular organisms, including humans, and the
processes that go on in these organisms. But remember, single-celled organisms carry
Question out all the essential functions of life too, only these occur within the single cell.
1 State the essential Cell size

processes
Cells are extremely small – most are only visible as distinct structures when we use
characteristic of
a microscope (although a few types of cells are just large enough to be seen by the
living things.
naked eye).
482876_01_Biology_001-030.indd 1 20/02/20 12:53 PM

Chlamydomonas – a motile, unicellular alga Amoeba – a protozoan of freshwater habitats
of freshwater habitats rich in ammonium ions cytoplasm
1 endoplasm clear ectoplasm
pseudopodia cell surface

flagella
contractile membrane
vacuole
nucleus
cytoplasm
1 Cell structure
length 400 lm
light-sensitive food vacuoles
spot chloroplast
Escherichia coli – a bacterium found in the intestines of animals, e.g. humans

nucleus
cell wall cell surface cytoplasm plasmid*
membrane
starch storage
length 30 lm
circular
length 2.0 lm DNA ribosomes
▲ Figure 1.1 Introducing unicellular organisation
*Plasmids are illustrated in Figure 1.25 (page 25) and in Figure 19.5 (page 463).
Observations of cells were first reported over 300 years ago, following the early
development of microscopes (see Figure 1.2). Today we use a compound light
microscope to investigate cell structure – perhaps you are already familiar with the light
microscope as a piece of laboratory equipment. You may have used one to view living
cells, such as the single-celled animal, Amoeba, shown in Figure 1.1.
Since cells are so small, we need suitable units to measure them. The
1 metre (m) = 1000 millimetres (mm) metre (symbol m) is the standard unit of length used in science. This is
1 mm = 1000 micrometres (μm) (or microns) an internationally agreed unit, or SI unit. Look at Table 1.1 – it shows
1 μm = 1000 nanometres (nm) the subdivisions of the metre that we use to measure cells and their
contents. These units are listed in descending order of size. You will see
▲ Table 1.1 Units of length used in microscopy 1
that each subdivision is 1000 of the unit above it. The smallest units are
probably quite new to you; they may take some getting used to.
The dimensions of cells are expressed in the unit called a micrometre or micron (μm).
Notice this unit is one thousandth (10 −3) of a millimetre. This gives us a clear idea
about how small cells are when compared to the millimetre, which you can see on a
standard ruler.
Bacteria are really small, typically 0.5–10 μm in size, whereas the cells of plants
and animals are often in the range 50–150 μm, or larger. In fact, the lengths of the
unicellular organisms shown in Figure 1.1 are approximately:
Chlamydomonas 30 μm

Amoeba 400 μm (but its shape and therefore length varies greatly)
Escherichia coli 2 μm
482876_01_Biology_001-030.indd 2 20/02/20 12:53 PM

Question 2 Calculate
a how many cells of 100 μm diameter will fit side by side along a millimetre 1
b the magnification of the image of Escherichia coli in Figure 1.1.
Hooke’s microscope, and a drawing

of the cells he observed

lens
position of
specimen
Robert Hooke (1635–1703), an expert mechanic and
one of the founders of the Royal Society in London, was
fascinated by microscopy. He devised a compound
microscope, and used it to observe the structure of cork.
He described and drew cork cells, and also measured
them. He was the first to use the term ‘cells’.
Anthony van Leeuwenhoek (1632–1723) was born

in Delft. Despite no formal training in science, he focus screws
developed a hobby of making lenses, which he side view
mounted in metal plates to form simple microscopes.
Magnifications of × 240 were achieved, and he observed
blood cells, sperms, protozoa with cilia, and even
bacteria (among many other types of cells). His results
were reported to the Royal Society, and he was elected
a fellow.
Robert Brown (1773–1858), a Scottish botanist, Leeuwenhoek’s microscope

observed and named the cell nucleus. He also observed
the random movements of tiny particles (pollen grains,
in his case) when suspended in water (Brownian motion). 2
1
Matthias Schleiden (1804–81) and Theodor Schwann
(1810–82), German biologists, established cells as the
natural unit of form and function in living things: ‘Cells
3
are organisms, and entire animals and plants are
aggregates of these organisms arranged to definite laws.’
Rudolf Virchow (1821–1902), a German pathologist,

established the idea that cells arise only by division of
existing cells.
Louis Pasteur (1822–95), a brilliant French

microbiologist, established that life does not
spontaneously generate. The bacteria that ‘appear’ in
broth are microbes freely circulating in the air, which Pasteur’s experiment, in which broth was sterilised (1),
contaminate exposed matter. and then either exposed to air (3) or protected from
air-borne spores in a swan-necked flask (2). Only the
broth in 3 became contaminated with bacteria.
▲ Figure 1.2 Early steps in the development of the cell theory
482876_01_Biology_001-030.indd 3 25/02/20 1:07 PM

Cell theory
1 Many biologists helped to develop the idea that living things are made of cells. This idea has
become known as the cell theory. This concept evolved gradually during the nineteenth
century, following a steadily accelerating pace in the development of microscopy and
biochemistry. You can see a summary of these developments in Figure 1.2.
Microscopy
A microscope is used to produce a magnified image of an object or specimen. Today,
cells can be observed by two fundamentally different types of microscopy:
1 Cell structure
» the compound light microscope, using visible light;

» the electron microscope, using a beam of electrons.
In this course you will be using the light microscope frequently, and we start here, using
it to observe temporary preparations of living cells. Later, we will introduce the electron
microscope and the changes this has brought to the study of cell structure.
Light microscopy
We use microscopes to magnify the cells of biological specimens in order to see them
at all. Figure 1.3 shows two types of light microscope. You do not need to know the
structure of a light microscope.
In the simple microscope (the hand lens), a single biconvex lens is held in a supporting
frame so that the instrument can be held close to the eye. Today a hand lens is used to
observe external structure. However, some of the earliest detailed observations of living
cells were made with single-lens instruments (see Figure 1.2).
In the compound microscope, light rays are focused by the condenser on to a
specimen on a microscope slide on the stage of the microscope. Light transmitted
through the specimen is then focused by two sets of lenses (hence the name ‘compound’
microscope). The objective lens forms an image (in the microscope tube) which is then
further magnified by the eyepiece lens, producing a greatly enlarged image.
using the simple
microscope
(hand lens)
You should bring the thing you

are looking at nearer to the lens
and not the other way round.
eyepiece lens using the

compound
microscope
turret – as it is turned the objectives

click into place, first the medium-
power, then the high-power
objective lenses – ×4 (low);

×10 (medium); ×40 (high power)
stage – microscope
coarse focus – used to focus the
slide placed here
low- and medium-power objectives
fine focus – used to focus condenser – focuses light on to

the high-power objective the object with iris diaphragm –
used to vary the intensity of light
reaching the object
built-in light source
▲ Figure 1.3 Light microscopy

4
482876_01_Biology_001-030.indd 4 25/02/20 1:11 PM

Cells and tissues examined with a compound microscope must be sufficiently
transparent for light rays to pass through. When bulky tissues and parts of organs are to
be examined, thin sections are cut. Thin sections are largely colourless. 1
Examining the structure of living cells
Living cells are not only tiny but also transparent. In light microscopy it is common
practice to add dyes or stains to introduce sufficient contrast and so differentiate
structure. Dyes and stains that are taken up by living cells are especially useful.
1 Observing the nucleus and cytoplasm in onion epidermis cells

A single layer of cells, known as the epidermis, covers the surface of a leaf. In the
circular leaf bases that make up an onion bulb, the epidermis is easily freed from the
cells below, and can be lifted away from a small piece of the leaf with fine forceps.
Place this tiny sheet of tissue on a microscope slide in a drop of water and add a
cover slip. Irrigate this temporary mount with iodine (I2/KI) solution (Figure 1.4). In
a few minutes the iodine will penetrate the cells, staining the contents yellow. The
nucleus takes up the stain more strongly than the cytoplasm, while the vacuole and
the cell walls are not stained at all.
Making a temporary mount Irrigating a temporary mount
mounted needle pipette blotting paper

a drop of stain placed
beside the cover slip
cover slip
microscope slide
stain drawn across,
cheek cell smear under the cover slip
▲ Figure 1.4 Preparing living cells for light microscopy
2 Observing chloroplasts in moss leaf cells

A leaf of a moss plant is typically mostly only one cell thick. Remove a leaf from
a moss plant, mount it in water on a microscope slide and add a cover slip. Then
examine individual cells under medium and high power magnification. No stain or
dye is used in this investigation.
What structures in these plant cells are visible?
3 Observing nucleus, cytoplasm and cell membrane in human cheek cells

Take a smear from the inside lining of your cheek, using a fresh, unused cotton
bud you remove from the pack. Touch the materials removed by the ‘bud’ on to the
centre of a microscope slide, and then immediately submerge your cotton bud in
1% sodium hypochlorite solution (or in absolute alcohol). Handle the microscope
slide yourself, and at the end of the observation immerse the slide in 1% sodium
hypochlorite solution (or in absolute alcohol). To observe the structure of human
cheek cells, irrigate the slide with a drop of methylene blue stain (Figure 1.4), and
examine some of the individual cells with medium and high power magnification.
How does the structure of these cells differ from plant cells?
4 Examining cells seen in prepared slides and in photomicrographs

The structures of cells can also be observed in prepared slides and in
photomicrographs made from prepared slides. You might choose to examine the
cells in mammalian blood smears and a cross-section of a flowering plant leaf, for
example. Alternatively (or in addition) you can examine photomicrographs of these
(Figure 8.6b on page 172 and Figure 7.2 on page 144).
5
482876_01_Biology_001-030.indd 5 25/02/20 1:09 PM

Recording observations
1 What you see with a compound microscope may be recorded by drawings of various
types. For a clear, simple drawing:
» use a sharp HB pencil and a clean eraser
» use unlined paper and a separate sheet for each specimen you record
» draw clear, sharp outlines and avoiding shading or colouring
» use most of the available space to show all the features observed in the specimen
» label each sheet or drawing with the species, conditions (living or stained),
transverse section (TS) or longitudinal section (LS), and so forth
1 Cell structure
» label your drawing fully, with labels positioned clear of the structures shown,
remembering that label lines should not cross
» annotate (add notes about function, role or development), if appropriate
» include a statement of the magnification under which the specimen has been
observed (for example, see pages 9–10).
view (phase contrast) of the layer of the The lining of the stomach consists of columnar
cells (epithelium) lining the stomach wall epithelium. All cells secrete mucus copiously.
columnar
epithelium cell
mucus
cytoplasm
nucleus
basement
membrane
▲ Figure 1.5 Recording cell structure by drawing
EXTENSION
Alternatively, images of cells and tissues viewed may be further magnified,
displayed or projected (and saved for printing out) by the technique of digital
microscopy. A digital microscope is used, or an appropriate video camera is
connected by a microscope coupler or eyepiece adaptor that replaces the standard
microscope eyepiece. Images are displayed via video recorder, TV monitor or
computer.
Calculating the linear magnification of drawings, photomicrographs

(and electron micrographs)
Since cells and the structures they contain are small, the images of cells and cell
structures (photographs or drawings) that we make are always highly magnified so that
the details of structure can be observed and recorded. Because of this, these images
typically show a scale bar to indicate the actual size of the cell or structure. Look at
Figure 1.6 – this is a case in point.
482876_01_Biology_001-030.indd 6 20/02/20 12:53 PM

photomicrograph of Amoeba proteus (living interpretive
interpretive drawing
drawing
specimen) – phase contrast microscopy
cell surface membrane
1
small food
vacuoles
pseudopodia

nucleus
large food vacuole
cytoplasm – outer,
clear (ectoplasm)
and inner, granular
(endoplasm)
contractile
vacuole
scale bar 0.1 mm
▲ Figure 1.6 Recording size by means of scale bars
From the scale bar we can calculate both the size of the image and the magnification of
the image.
1 Size of the Amoeba in Figure 1.6

Use a ruler to measure the length of the image of cell. This is 78 mm.
Use a ruler to measure the length of the scale bar. This is 16 mm.
(Note that the scale represents an actual length of 0.1 mm.)
It is very important in these calculations to make sure that the units for the size of the
image and the actual size of the specimen are the same – either millimetres (mm) or
micrometres (μm). Millimetres can be converted to micrometres by multiplying by one
thousand. Micrometres can be converted to millimetres by dividing by one thousand.
So:
The length of the image of the cell is 78 × 1000 μm = 78 000 μm
The length of the scale bar is 16 × 1000 μm = 16 000 μm
The scale represents an actual length of 0.1 × 1000 μm = 100 μm
We use the ratio of these values to work out the actual length of the Amoeba.
100 µm actual length of the cell
=
16 000 µm 78 000 µm
78 000 µm
actual length = 100 μm ×
16 000 µm
= 488 μm
(Note that Amoeba moves about by streaming movements of its cytoplasm. In this image the cell
is extended and its length seems large, perhaps. It is equally likely to be photographed in a more
spherical shape, of diameter one tenth of its length here.)
2 Magnification of the Amoeba

measured size of the cell
We use the formula: magnification =
actual length of the cell
78 000 µm
So here: magnification = = ×160
488 µm
7
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Question 3 Finally, given the magnification of an image, we can calculate
its real size
1 3 Using the
magnification
Look at the images of the human cheek cell in Figure 1.22 (page 21).
Measure the observed length of the cell in mm. It is 75 mm.
given for the
Convert this length to μm: 75 mm = 75 × 1000 μm = 75 000 μm
photomicrograph
of the cell of Elodea image size (I) 75000
Use the equation: actual size (A) = = × 190
= 93.8 μm
in Figure 1.22 magnification (M) × 800
(page 21), calculate This size is greater than many human cheek cells. It suggests these epithelial cells are
the actual length of squashed flat in the position they have in the skin, perhaps.
1 Cell structure
the cell.
Measuring microscopic objects
The size of a cell can be measured under the microscope. A transparent scale called a
graticule is mounted in the eyepiece at a point called the focal plane. There is a ledge for
it to rest on. In this position, when the object under observation is in focus, so too is the
scale. The size (e.g. length, diameter) of the object may then be recorded in arbitrary units.
compound light eyepiece

microscope
turret with
medium- and high- 0 1 2 3 4 5 6 7 8 9 10
power objectives
shelf –
stage the eyepiece
coarse and graticule is
fine focus installed here
controls
built-in light
source
with iris graticule much
diaphragm enlarged – scale
is arbitrary units
1 Measuring a cell (e.g. a red blood cell)
by alignment with the scale on the
eyepiece graticule
using a prepared red blood cell (side view)

slide of mammalian with the eyepiece graticule
blood smear 0 1 2 3 4 5 6 7 8 9 10 0 1 2 scale superimposed
red blood cell diameter

measured
(arbitrary units)
2 Calibrating the graticule scale

by alignment of graticule and
stage micrometer scales
0 1 2 3 4 5 6 7 8 9 10
the stage micrometer is placed on the

stage in place of the prepared slide and
examined at the same magnification
now graticule scale and stage micrometer the measurement of the red
scale are superimposed blood cell diameter is converted
to a μm measurement
0 1 2
1.5 (15 units) in this case, the red blood

cell appears to have a
diameter of about 8 μm
0 10 μm
▲ Figure 1.7 Measuring the size of cells
482876_01_Biology_001-030.indd 8 25/02/20 1:59 PM

Next, the graticule scale is calibrated using a stage micrometer. This is a tiny,
transparent ruler which is placed on the microscope stage in place of the slide and then
observed. With the graticule and stage micrometer scales superimposed, the actual
dimensions of the object can be estimated in microns. Figure 1.7 shows how this is
1
done. Once the size of a cell has been measured, a scale bar line may be added to a
micrograph or drawing to record the actual size of the structure, as illustrated in the
photomicrograph in Figure 1.6. Alternatively, the magnification can be recorded.
The magnification and resolution of an image

Magnification is the number of times larger an image is than the specimen. The
magnification obtained with a compound microscope depends on which of the lenses
you use. For example, using a ×10 eyepiece and a ×10 objective lens (medium power),
the image is magnified ×100 (10 × 10). When you switch to the ×40 objective lens
(high power) with the same eyepiece lens, then the magnification becomes ×400
(10 × 40). These are the most likely orders of magnification used in your
laboratory work.
Actually, there is no limit to magnification. For example, if a magnified image is
photographed, then further enlargement can be made photographically. This is what
may happen with photomicrographs shown in books and articles.
size of image
Magnification is given by the formula:
size of specimen
So, if a particular plant cell with a diameter of 150 μm is photographed with a

microscope and the image is enlarged photographically, so that in a print of the cell the
150 000
diameter is 15 cm (150 000 μm), the magnification is: = 1000.
150
If a further enlargement is made, to show the same cell at a diameter of 30 cm
300 000
(300 000 μm), then the magnification is: = 2000.
150
In this particular case the image size has been doubled, but the detail will be no
greater. You will not be able to see, for example, details of cell surface membrane
structure however much the image is enlarged. This is because the layers making
up a cell’s membrane are too thin to be seen as separate structures using the light
microscope.
The resolving power (resolution) of a microscope is its ability to separate small objects
that are very close together. If two separate objects cannot be resolved they will be seen
as one object. Merely enlarging them will not separate them.
The resolution achieved by a light microscope is determined by the wavelength of light.
Visible light has a wavelength in the range 400–700 nm. (By ‘visible’ we mean our eyes
and brain can distinguish light of wavelength of 400 nm (violet light) from light of
wavelength of 700 nm, which is red light.)
Question
In a microscope, the limit of resolution is approximately half the wavelength of
4 Calculate the light used to view the object. So, any structure in a cell that is smaller than half the
magnification wavelength of light cannot be distinguished from nearby structures. For the light
obtained with a ×6 microscope the limit of resolution is about 200 nm (0.2 μm). This means two objects less
eyepiece and a ×10 than 0.2 μm apart may be seen as one object.
objective lens.
To improve on this level of resolution the electron microscope is required (Figure 1.8).
482876_01_Biology_001-030.indd 9 20/02/20 12:54 PM

chloroplast enlarged (× 6000) a) from a b) from a transmission electron
photomicrograph obtained by light microscopy micrograph
1
1 Cell structure
▲ Figure 1.8 Magnification a) without and b) with resolution
Electron microscopy – the discovery of cell ultrastructure

The electron microscope uses electrons to make a magnified image in much the same
way as the light microscope uses light. However, because an electron beam has a much
shorter wavelength its resolving power is much greater. For the electron microscope
used with biological materials, the limit of resolution is about 5 nm. (The size of a
nanometre is given in Table 1.1 on page 2.)
Only with the electron microscope can the detailed structure of the cell organelles
be observed. This is why the electron microscope is used to resolve the fine detail of
the contents of cells. The fine detail of cell structure is called cell ultrastructure. It is
Question difficult to exaggerate the importance of electron microscopy in providing our detailed
knowledge of cells.
5 Distinguish between
‘resolution’ and Figure 1.9 shows an electron microscope. In an electron microscope, the electron beam
‘magnification’. is generated by an electron gun, and focusing is by electromagnets, rather than glass
lenses. We cannot see electrons, so the electron beam is focused on to a fluorescent
screen for viewing or on to a photographic plate for permanent recording. You do not
need to know the structure of an electron microscope.
a) b)
air lock/specimen port

electron gun the specimen is introduced without
emits an accelerated the loss of vacuum
electron beam
condenser
electromagnetic lens
focuses the electron objective
beam on to specimen electromagnetic lens that focuses
the first image (according to voltage)
specimen
position projector
electromagnetic lens that magnifies a
part of the first image
vacuum viewing port

pump with binocular viewer
fluorescent screen
coated with electron-sensitive compound
camera chamber
Electrons are negatively charged and are allows a black and white photographic
easily focused using electromagnets. image to be made (with the possibility
transmission electron microscope of further magnification)
▲ Figure 1.9 Using the transmission electron microscope
10
482876_01_Biology_001-030.indd 10 25/02/20 1:10 PM

EXTENSION
Limitations of the electron microscope – and how these are overcome
1
The electron microscope has revolutionised the study of cells. It has also changed
the way cells can be observed. The electron beam travels at very high speed but at
very low energy. This has practical consequences for the way biological tissue is
observed at these very high magnifications and resolution.
Next we look into these outcomes and the way the difficulties are overcome.

1 Electrons cannot penetrate materials as well as light does
Specimens must be extremely thin for the electron beam to penetrate and for some of
the electrons to pass through. Biological specimens are sliced into very thin sections
using a special machine called a microtome. Then the membranes and any other tiny
structures present in these sections must be stained with heavy metal ions (such as
lead or osmium) to make them absorb electrons at all. (We say they become electron-
opaque.) Only then will these structures stand out as dark areas in the image.
2 A
ir inside the microscope would deflect the electrons and
destroy the beam
The interior of the microscope must be under a vacuum. Because of the vacuum,
no living specimens can survive inside the electron microscope when in use.
Water in cells would boil away in a vacuum.
As a result, before observations are possible, a specimen must have all the water
removed. Sections are completely dehydrated. This has to be done while keeping
the specimen as ‘life-like’ in structure as is possible. This is a challenge, given
that cells are 80–90 per cent water. It is after the removal of water that the
sections have the electron-dense stains added.
The images produced when this type of section is observed by the electron
microscope are called transmission electron micrographs (TEMs) (Figure 1.10).
TEM of liver cells (×15 000)
interpretive drawing
nucleus – controls
and directs the
activities of the cell
Question
ribosomes
6 Given the
mitochondria
magnification of the
rough
TEM of a liver cell in endoplasmic lysosomes
Figure 1.10, calculate reticulum (RER)
a the length of the vesicles Golgi apparatus
cell
b the diameter of
the nucleus. ▲ Figure 1.10 Transmission electron micrograph of a liver cell, with interpretive drawing
11
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In an alternative method of preparation, biological material is instantly frozen solid in
liquid nitrogen. At atmospheric pressure this liquid is at −196°C. At this temperature
1 living materials do not change shape as the water present in them solidifies instantly.
This solidified tissue is then broken up in a vacuum and the exposed surfaces are
allowed to lose some of their ice. The surface is described as ‘etched’.
Finally, a carbon replica (a form of ‘mask’) of this exposed surface is made and
coated with heavy metal to strengthen it. The mask of the surface is then examined
in the electron microscope. The resulting electron micrograph is described as being
produced by freeze etching.
1 Cell structure
A comparison of a cell nucleus prepared as a thin section and by freeze etching

is shown in Figure 1.11. The picture we get of nucleus structure is consistent. It
explains why we can be confident that our views of cell structure obtained by electron
microscopy are realistic.
observed as thin section replica of freeze-etched surface
the nucleus of a
liver cell
nuclear membrane
(a double membrane)
nuclear membrane
with pores
cytoplasm with
mitochondria
▲ Figure 1.11 Transmission electron micrographs from thin-sectioned and freeze-etched material
An alternative form of electron microscopy is scanning electron microscopy. In

this, a narrow electron beam is scanned back and forth across the surface of the
whole specimen. Electrons that are reflected or emitted from this surface are detected
and converted into a three-dimensional image. Larger specimens can be viewed by
scanning electron microscopy rather than by transmission electron microscopy, but
the resolution is not as great (see Figure 1.12).
Streptococcus pyogenes red blood cells

(0.7 μm in diameter) (5.7 μm in diameter)
▲ Figure 1.12 Scanning electron micrographs
12
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1.2 Cells as the basic units of living organisms
The cell is the basic unit Learning outcomes 1
of all living organisms. The
interrelationships between
these cell structures show 1.2.1 recognise organelles and other cell structures found in eukaryotic
how cells function to cells and outline their structures and functions, limited to: cell surface
transfer energy, produce membrane; nucleus, nuclear envelope and nucleolus; rough endoplasmic
biological molecules reticulum; smooth endoplasmic reticulum; Golgi body (Golgi apparatus
including proteins and or Golgi complex); mitochondria (including the presence of small circular

exchange substances DNA); ribosomes (80S in the cytoplasm and 70S in chloroplasts and
with their surroundings. mitochondria); lysosomes; centrioles and microtubules; cilia; microvilli;
Prokaryotic cells and chloroplasts (including the presence of small circular DNA); cell wall;
eukaryotic cells share
plasmodesmata; and large permanent vacuole and tonoplast of plant cells
some features, but the
differences between 1.2.2 describe and interpret photomicrographs, electron micrographs and
them illustrate the divide drawings of typical plant and animal cells
between these two cell 1.2.3 compare the structure of typical plant and animal cells
types. 1.2.4 state that cells use ATP from respiration for energy-requiring processes
1.2.5 outline key structural features of a prokaryotic cell as found in a
typical bacterium, including: unicellular, generally 1–5 μm diameter,
peptidoglycan cell walls, circular DNA, 70S ribosomes, and absence of
organelles surrounded by double membranes
1.2.6 compare the structure of a prokaryotic cell as found in a typical bacterium
with the structures of typical eukaryotic cells in plants and animals
1.2.7 state that all viruses are non-cellular structures with a nucleic acid core
(either DNA or RNA) and a capsid made of protein, and that some viruses
have an outer envelope made of phospholipids
Today we recognise that the statement that cells are the unit of structure and function in
living things really contains three basic ideas.
» Cells are the building blocks of structure in living things.
» Cells are the smallest unit of life.
» Cells are made from other cells (pre-existing cells) by division.
To this we can now confidently add two concepts.
» Cells contain a blueprint (information) for their growth, development and behaviour.
» Cells are the site of all the chemical reactions of life (metabolism).
No ‘typical’ cell exists – there is great variety among cells. However, we shall see
that most cells have features in common. Using a compound microscope, the initial
appearance of a cell is of a sac of fluid material, bound by a membrane and containing a
nucleus.
A cell consists of a nucleus surrounded by cytoplasm, contained within the cell
surface membrane. The nucleus is the structure that controls and directs the activities
of the cell. The cytoplasm is the site of the chemical reactions of life, which we call
‘metabolism’. The cell surface membrane, sometimes called the plasma membrane, is
the barrier controlling entry to and exit from the cytoplasm.
Animal and plant cells have these three structures in common. In addition, there are many
tiny structures in the cytoplasm, called organelles. Most of these organelles are found
in both animal and plant cells. An organelle is a discrete structure within a cell, having
a specific function. Organelles are all too small to be seen at this magnification. We have
learnt about the structure of organelles using the electron microscope (see page 10).
There are some important basic differences between plant and animal cells. For
example, there is a tough, slightly elastic cell wall, made largely of cellulose, present
around plant cells. Cell walls are absent from animal cells.
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Question A vacuole is a fluid-filled space within the cytoplasm, surrounded by a single
membrane. Plant cells frequently have a large permanent vacuole. By contrast, animal
1 7 Draw up a table
to highlight the
cells may have small vacuoles, and these are often found to be temporary structures.
Green plant cells contain organelles called chloroplasts in their cytoplasm. These are
differences between
not found in animal cells. Chloroplasts are where green plant cells manufacture food
plant and animal
cells. molecules by a process known as photosynthesis.
The centrosome, an organelle that lies close to the nucleus in animal cells, is not present
in plants. This tiny organelle is involved in nuclear division in animal cells (see page 116).
1 Cell structure
Finally, the way organisms store energy-rich reserves differs, too. Animal cells may store
glycogen (see page 41); plants cells normally store starch (see page 40).
Studying cell structure by electron microscopy

Look back at Figure 1.10 (on page 11). Here the organelles of a liver cell are shown in a
transmission electron micrograph (TEM) and identified in an interpretive diagram. You
can see immediately that many organelles are made of membranes – but not all of them.
In the living cell there is a fluid around the organelles. The cytosol is the aqueous (watery)
part of the cytoplasm in which the organelles are suspended. The chemicals in the cytosol
are substances formed and used in the chemical reactions of life. All the reactions of life
are known collectively as metabolism, and the chemicals are known as metabolites.
Cytosol and organelles are contained within the cell surface membrane. This
membrane is clearly a barrier of sorts. It must be crossed by all the metabolites that
move between the cytosol and the environment of the cell.
Cytosol, organelles and the cell surface membrane make up a cell – a unit of structure
and function which is remarkably able to survive, prosper and replicate itself. The
molecules present in cells and how the chemical reactions of life are regulated are the
Question
subject of Topic 2. The structure of the cell membrane and how molecules enter and
8 Outline how the leave cells is the subject of Topic 4.
electron microscope
The structure and function of the organelles is what we consider next. Our
has increased our
understanding of organelles has been built up by examining TEMs of very many
knowledge of cell
structure. different cells. The outcome, a detailed picture of the ultrastructure of animal and plant
cells, is represented diagrammatically in a generalised cell in Figure 1.13.
Organelle structure and function

The electron microscope has enabled us to see and understand the structure of the
organelles of cells. However, looking at detailed structure does not tell us what the
individual organelles do in the cell. This information we now have, too. This is because
it has been possible to isolate working organelles and analyse the reactions that go on in
them and the enzymes they contain. In other words, investigations of the biochemical
roles of organelles have been undertaken. Today we know about the structure and
function of the cell organelles.
1 Cell surface membrane

The cell surface membrane is an extremely thin structure – less than 10 nm thick. It
consists of a lipid bilayer in which proteins are embedded (Figure 4.3, page 83). At very
high magnification it can be seen to have three layers – two dark lines (when stained)
separated by a narrow gap (Figure 4.4, page 83).
The detailed structure and function of the cell surface membrane is the subject of Topic 4.
In outline, the functions are as follows. Firstly, it retains the fluid cytosol. The cell surface
membrane also forms the barrier across which all substances entering and leaving the cell
must pass. In addition, it is where the cell is identified by surrounding cells.
14
482876_01_Biology_001-030.indd 14 20/02/20 12:54 PM

animal cell plant cell
rough endoplasmic
Golgi apparatus
1
free ribosomes free ribosomes reticulum (RER)
with ribosomes
attached
lysosome
chloroplast

smooth lysosome
endoplasmic
reticulum
(SER)
mitochondrion
centrioles
smooth
mitochondrion endoplasmic
reticulum (SER)
rough
endoplasmic
reticulum
(RER) with
ribosomes cell surface
attached membrane
cell surface cellulose

membrane cell wall
temporary vacuoles nucleolus permanent vacuole

nuclear envelope chromatin
formed by intucking
of plasma membrane nucleus
▲ Figure 1.13 The ultrastructure of the eukaryotic animal and plant cell
2 Nucleus, nuclear envelope and nucleolus

The appearance of the nucleus in electron micrographs is shown in Figures 1.10
(page 11) and 1.11 (page 12). The nucleus is the largest organelle in the eukaryotic
cell, typically 10–20 μm in diameter. It is surrounded by two membranes, known
as the nuclear envelope. The outer membrane is continuous with the endoplasmic
reticulum. The nuclear envelope contains many pores. These are tiny, about 100 nm
in diameter. However, they are so numerous that they make up about one-third of the
nuclear membrane’s surface area. The function of the pores is to make possible speedy
movement of molecules between nucleus and cytoplasm (such as messenger RNA), and
between cytoplasm and the nucleus (such as proteins, ATP and some hormones).
The nucleus contains the chromosomes. These thread-like structures are made of DNA
and protein, and are visible at the time the nucleus divides (page 116). At other times,
the chromosomes appear as a diffuse network called chromatin.
Also present in the nucleus is a nucleolus. This is a tiny, rounded, darkly-staining body.
It is the site where ribosomes (see next page) are synthesised. Chromatin, chromosomes
and the nucleolus are visible only if stained with certain dyes.
The everyday role of the nucleus in cell management, and its behaviour when the cell
divides, are the subject of Topic 5. Here we can note that most cells contain one nucleus
but there are interesting exceptions. For example, both the mature red blood cells of
mammals and the sieve tube elements of the phloem of flowering plants are without
15
482876_01_Biology_001-030.indd 15 20/02/20 12:54 PM

a nucleus. Both lose their nucleus as they mature. The individual cylindrical fibres of
voluntary muscle consist of a multinucleate sack (page 255). Fungal mycelia also contain
1 multinucleate cytoplasm.
3 Endoplasmic reticulum
The endoplasmic reticulum consists of a network of folded membranes formed into
sheets, tubes or sacs that are extensively interconnected. Endoplasmic reticulum ‘buds
off’ from the outer membrane of the nuclear envelope, to which it may remain attached.
The cytoplasm of metabolically active cells is commonly packed with endoplasmic
reticulum. In Figure 1.14 we can see there are two distinct types of endoplasmic
1 Cell structure
reticulum.
» Rough endoplasmic reticulum (RER) has ribosomes attached to the outer surface.
At its margin, vesicles are formed from swellings. A vesicle is a small, spherical
organelle bounded by a single membrane, which becomes pinched off as they
separate. These tiny sacs are then used to store and transport substances around the
cell. For example, RER is the site of synthesis of proteins that are ‘packaged’ in the
vesicles. These vesicles then fuse with the Golgi apparatus and are then typically
discharged from the cell. Digestive enzymes are discharged in this way.
» Smooth endoplasmic reticulum (SER) has no ribosomes. SER is the site of
synthesis of substances needed by cells. For example, SER is important in the
manufacture of lipids and steroids, and the reproductive hormones oestrogen and
testosterone. In the cytoplasm of voluntary muscle fibres, a special form of SER is
the site of storage of calcium ions, which have an important role in the contraction
of muscle fibres.
SER and RER in cytoplasm, showing origin from outer membrane of nucleus TEM of RER
ribosomes rough vesicles pinched off
endoplasmic with proteins/enzymes
reticulum for export from cell
nucleus
roles of endoplasmic reticulum
vesicles with
steroid hormones
TEM of SER
vesicles with enzymes

to deactivate toxins
site of storage of calcium ions

smooth endoplasmic in (relaxed) voluntary muscle
reticulum
▲ Figure 1.14 The structure of endoplasmic reticulum – rough (RER) and smooth (SER)
16
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4 Golgi apparatus
The Golgi apparatus (Golgi body, Golgi complex) consists of a stack-like collection of
flattened membranous sacs. One side of the stack of membranes is formed by the fusion 1
of membranes of vesicles from RER or SER. At the opposite side of the stack, vesicles are
formed from swellings at the margins that again become pinched off. The structure of
the Golgi apparatus is shown in Figure 1.15.
TEM of Golgi apparatus, in section
a)
vesicles pinched

off here
stack of flattened,
membranous sacs
▲ Figure 1.15 The structure of the Golgi apparatus
a mitochondrion, cut open

to show the inner membrane and cristae
The Golgi apparatus occurs in all cells, but it is especially prominent in
metabolically active cells – for example, secretory cells. More than one may
be present in a cell. It is the site of synthesis of specific biochemicals, such
outer membrane
as hormones, enzymes or others. Here specific proteins may be activated
inner membrane by addition of sugars (forming glycoprotein) or by the removal of the
matrix amino acid, methionine. These are then packaged into vesicles. In animal
cristae cells these vesicles may form lysosomes. Those in plant cells may contain
polysaccharides for cell wall formation.
5 Mitochondria
In the mitochondrion many respiration Mitochondria appear mostly as rod-shaped or cylindrical organelles in
enzymes are housed, and the ‘energy currency’
molecules of adenosine triphosphate (ATP) are formed. electron micrographs. Occasionally their shape is more variable. They are
TEM of a thin section of relatively large organelles, typically 0.5–1.5 μm wide, and 3.0–10.0 μm
a mitochondrion long. Mitochondria are found in all cells and are usually present in very
large numbers. Metabolically very active cells will contain thousands of
them in their cytoplasm – for example, in muscle fibres and hormone-
secreting cells.
The mitochondrion also has a double membrane (Figure 1.16). The outer
membrane is a smooth boundary, the inner is infolded to form cristae. The
interior of the mitochondrion is called the matrix. It contains an aqueous
solution of metabolites and enzymes, and also small circular lengths of
DNA. The mitochondrion is the site of the aerobic stages of respiration and
the site of the synthesis of much ATP (see page 22).
Mitochondria (and chloroplasts) contain ribosomes, too. They appear as
tiny dark dots in the matrix of the mitochondria, and are slightly smaller
than the ribosomes found in the cytosol and attached to RER.
▲ Figure 1.16 The structure

of the mitochondrion
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482876_01_Biology_001-030.indd 17 20/02/20 12:55 PM

6 Ribosomes
1 Ribosomes are minute structures, approximately 25 nm in diameter. They are built of

two sub-units, and do not have membranes as part of their structures. Chemically, they
consist of protein and a nucleic acid known as RNA (ribonucleic acid). The sizes of tiny
objects like ribosomes are recorded in Svedberg units (S). This is a measure of their rate
of sedimentation in centrifugation, rather than their actual size. The smaller ribosomes
found in mitochondria and chloroplasts are 70S; the larger 80S ribosomes are found free
in the cytosol or bound to endoplasmic reticulum. We return to the significance of this
discovery later in the topic (the endosymbiotic theory, page 26).
1 Cell structure
Ribosomes are the sites where proteins are made in cells. The structure of a ribosome
is shown in Figure 6.15, page 134, where their role in protein synthesis is illustrated.
Many different types of cell contain vast numbers of ribosomes. Some of the cell
proteins produced in the ribosomes have structural roles. Collagen is an example (page
53). A great many other cell proteins are enzymes. These are biological catalysts. They
cause the reactions of metabolism to occur quickly under the conditions found within
the cytoplasm.
Question 9 Explain why the nucleus in a human cheek cell (see Figure 1.22, page 21) may
be viewed by light microscopy in an appropriately stained cell but the
ribosomes cannot.
7 Lysosomes
Lysosomes are tiny spherical vesicles bound by a single membrane. They contain a
concentrated mixture of ‘digestive’ enzymes. These are correctly known as hydrolytic
enzymes. They are produced in the Golgi apparatus or by the RER.
Lysosomes are involved in the breakdown of the contents of ‘food’ vacuoles. For
example, harmful bacteria that invade the body are taken up into tiny vacuoles (they are
engulfed) by special white cells called macrophages. Macrophages are part of the body’s
defence system (see Topic 11).
Any foreign matter or food particles taken up into these vacuoles are then broken down.
This occurs when lysosomes fuse with the vacuole. The products of digestion then
escape into the liquid of the cytoplasm. Lysosomes will also destroy damaged organelles
in this way.
When an organism dies, the hydrolytic enzymes in the lysosomes of the cells escape
into the cytoplasm and cause self-digestion, known as autolysis.
undigested remains
discharged from cell
digestion occurs; useful
products of digestion
absorbed into cytosol
of cell food vacuole
formed at cell
membrane (phagocytosis)
defunct lysosome fuses

organelle (bringing hydrolytic
enzymes into vacuole)
vesicles of hydrolytic
enzymes (lysosomes)
cut off from Golgi
apparatus
steps in the
formation of vesicles from SER and
a lysosome RER fuse to form flattened
membranous sacs of the
Golgi apparatus
▲ Figure 1.17 The structure and function of lysosomes

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8 Centrioles and microtubules
A centriole is a tiny organelle consisting of nine paired microtubules arranged in a
short, hollow cylinder. In animal cells, two centrioles occur at right angles, just outside 1
the nucleus, forming the centrosome. Before an animal cell divides the centrioles
replicate, and their role is to grow the spindle fibres – structures responsible for
movement of chromosomes during nuclear division.
Microtubules themselves are straight, unbranched hollow cylinders, only 25 nm wide.
They are made of a globular protein called tubulin. This is first built up and then later
broken down in the cell as the microtubule framework is required in different places for

different tasks.
The cells of all eukaryotes, whether plants or animals, have a well-organised system of
these microtubules, which shape and support the cytoplasm. Microtubules are involved
▲ Figure 1.18 The in movements of cell components within the cytoplasm, too, acting to guide and direct
structure of the organelles.
centrosome
9 Cilia
Cilia are organelles that project from the surface of certain cells. They can move and can
EXTENSION be up to 10 μm long. Cilia occur in large numbers on certain cells, such as the ciliated
lining (epithelium) of the air tubes serving the lungs (bronchi), where they cause the
Flagella movement of mucus across the cell surface, shown in Figure 9.3 on page 190.
Structurally, cilia and
flagella are almost 10 Microvilli
identical, and both Microvilli are minute projections, around 1 μm long, from the surface of some cells
can move. Flagella formed by the infoldings of the plasma membrane, making a ‘brush border’. Although
occur singly, typically microvilli are cellular extensions, few cellular organelles are present. They increase
on small, motile cells, the surface area enormously for functions such as absorption, for example in the small
such as sperm, or they intestine and in the proximal convoluted tubule of the kidney (see page 305).
may occur in pairs.
11 Chloroplasts
Chloroplasts are large organelles, typically biconvex in shape, about 4–10 μm long and
2–3 μm wide. They occur in green plants, where most occur in the mesophyll cells of
leaves. A mesophyll cell may be packed with 50 or more chloroplasts. Photosynthesis is
the process that occurs in chloroplasts and is the subject of Topic 13.
Look at the chloroplasts in the TEM in Figure 1.19. Each chloroplast has a double
membrane. The outer layer of the membrane is a continuous boundary, but the inner
layer becomes in-tucked to form a system of branching membranes called lamellae or
thylakoids. In some regions of the chloroplast the thylakoids are arranged in flattened
circular piles called grana (singular: granum). These look a little like a stack of coins. It
is here that the chlorophylls and other pigments are located. There are a large number
of grana present. Between them the branching thylakoid membranes are very loosely
arranged. The fluid outside the thylakoid is the stroma, which contains small circular
DNA and ribosomes (70S), together with many enzymes.
Chloroplasts are the site of photosynthesis by which light is used as the energy source in
carbohydrate and ATP synthesis (see page 22).
▲ Figure 1.19 TEM of a thin 12 Cell wall and plasmodesmata

section of chloroplasts
A cell wall is a structure external to a cell, and is therefore not an organelle, although
it is the product of cell organelles. The presence of a rigid external cell wall is a
characteristic of plant cells. Plant cell walls consist of cellulose together with other
19
482876_01_Biology_001-030.indd 19 20/02/20 12:55 PM

plasmodesma cellulose substances, mainly other polysaccharides, and are fully permeable. Cell walls are
cell wall secreted by the cell they enclose, and their formation and composition are closely tied
1 in with the growth, development and functions of the cell they enclose, support and
protect.
Plasmodesmata (singular: plasmodesma) are the cytoplasmic connections between
cells, running transversely through the walls, connecting the cytoplasm and adjacent
vacuole cytoplasm
cells. Plasmodesmata are formed when a cell divides and lays down new walls between
pathways through the separating cell contents (Figure 1.20). Typically, the cytoplasm of plasmodesmata
the cytoplasm includes endoplasmic reticulum, and occupies the holes or pits between adjacent cells.
1 Cell structure
▲ Figure 1.20 They are part of the symplast pathway (see page 151) through which, for example,
Plasmodesmata develop inorganic ions are able to pass from cell to cell without having to pass through cell walls
as new cell walls form or cell surface membranes.
between plant cells
13 Large permanent vacuole of plant cells and the tonoplast
We have seen that the plant cell is surrounded by a tough but flexible external cell wall.
The cytoplasm and cell membrane are pressed firmly against the wall by a large, fluid-
filled permanent vacuole that takes up the bulk of the cell (Figure 1.21). The vacuole is
surrounded by a specialised membrane, the tonoplast. This is the barrier between the
fluid contents of the vacuole (sometimes called ‘cell sap’) and the cytoplasm.
▲ Figure 1.21 TEM of a mesophyll cell of Zinnia,

showing a large central vacuole and chloroplasts
within the cytoplasm (×3800)
Question 10 We have seen that analyses of TEM images of cells have played an important part
in the discovery of cell ultrastructure. Carefully examine the image of a green plant
cell shown in the TEM in Figure 1.21. Using the interpretive drawing in Figure 1.10
(page 11) as a model and following the guidelines on biological recording on page 6,
draw and label a representation of the green plant cell shown in Figure 1.21.
Comparison of typical plant and animal cells

Question
Figure 1.22 shows two cells viewed using a compound light microscope. One is a plant
11 What are the cell, the other a human cell. Cell walls and chloroplasts are visible in the plant cells,
difficulties in trying while the nucleus and granules are visible in the human cell. The organelles are all too
to describe a typical small to be seen at this magnification.
plant or animal cell?
Table 1.2 outlines the important basic differences between plant and animal cells.
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Feature Plant cells Animal cells
Cell wall Cellulose cell wall present No cellulose cell wall 1
Chloroplasts Many cells contain chloroplasts; site of No chloroplasts; animal cells cannot
photosynthesis photosynthesize
Permanent vacuole Large, fluid-filled vacuole typically present No large permanent vacuoles
Centrosome No centrosome A centrosome present outside the nucleus
Carbohydrate storage product Starch Glycogen

▲ Table 1.2 Basic differences between plant and animal cells
Canadian pondweed (Elodea) human

grows submerged in fresh water
1m
5 cm
photomicrograph of a leaf cell of Elodea photomicrograph of a human cheek cell

(×400) (×800)
large permanent vacuole,

surrounded by a membrane secretory
granules
cellulose cell wall

cytoplasm temporary
vacuoles
cell surface
membrane
pit where the cytoplasm

of cells connects
(plasmodesma) nucleus
centrosome
chloroplasts
(with starch grains)
junction between cell

walls (the middle lamella)
▲ Figure 1.22 Plant and animal cells from multicellular organisms

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ATP, its production in mitochondria and chloroplasts,
1 and its role in cells
ATP (adenosine triphosphate) is the universal energy currency molecule of cells.
ATP is formed from adenosine diphosphate (ADP) and a phosphate ion (Pi) by the
transfer of energy from other reactions. ATP is referred to as ‘energy currency’ because,
like money, it can be used in different contexts, and it is constantly recycled. It occurs
in cells at a concentration of 0.5–2.5 mg cm−3. ATP is a relatively small, water-soluble
organic molecule, able to move easily around cells, that effectively transfers energy in
relatively small amounts, sufficient to drive individual reactions.
1 Cell structure
ATP is a nucleotide with an unusual feature. It carries three phosphate groups linked
together in a linear sequence. ATP may lose both of the outer phosphate groups, but
usually only one at a time is lost.
phosphate
adenine phosphate phosphate
ribose
adenosine triphosphate ATP

adenosine diphosphate ADP
adenosine monophosphate AMP
ATP is formed during sugar + oxygen carbon dioxide

respiration (and in + water
photosynthesis) resp
ir a ti o n
ADP + Pi ATP
tosynthesis
pho
+H2O
light energy via photophosphorylation
metabolic reactions and metabolic processes driven

by energy transferred from ATP, e.g.
• movement of materials across cell membranes
• building molecules, including macromolecules
and other biomolecules
• movements by muscle contraction, and other
cellmovements
▲ Figure 1.23 ATP and the ATP–ADP cycle
ATP contains a good deal of chemical energy locked up in its structure. What makes
ATP special as a reservoir of stored chemical energy is its role as a common intermediate
between energy-yielding reactions and energy-requiring reaction and processes.
» Energy-yielding reactions include the photophosphorylation reactions of
photosynthesis, and the reactions of cell respiration in which sugars are broken
down and oxidised.
» Energy-requiring reactions include the synthesis of cellulose from glucose, the
synthesis of proteins from amino acids, the contractions of muscle fibres, and the
active transport of certain molecules across cell membranes, for example.
22
482876_01_Biology_001-030.indd 22 20/02/20 12:55 PM

» The free energy available in the conversion of ATP to ADP is approximately
30–34 kJ mol−1, made available in the presence of a specific enzyme. Some of this
energy is lost as heat in a reaction, but much free energy is made available to do 1
useful work, more than sufficient to drive a typical energy-requiring reaction of
metabolism.
» Sometimes ATP reacts with water (a hydrolysis reaction) and is converted to ADP and
Pi. Direct hydrolysis of the terminal phosphate groups like this happens in muscle
contraction, for example.
» Mostly, ATP reacts with other metabolites and forms phosphorylated intermediates,
Question making them more reactive in the process. The phosphate groups are released later,

12 Outline why ATP is so both ADP and Pi become available for reuse as metabolism continues.
an efficient energy In summary, ATP is a molecule universal to all living things; it is the source of energy
currency molecule. for chemical change in cells, tissues and organisms.
Prokaryotic and eukaryotic cells

Finally, we need to introduce a major division that exists in the structure of cells. The
discovery of two fundamentally different types of cell followed on from the application
of the electron microscope to the investigation of cell structure.
All plants, animals, fungi and protoctista (these are the single-celled organisms, such
as Amoeba and the algae) have cells with a large, obvious nucleus. There are several
individual chromosomes within the nucleus, which is a relatively large spherical sac
bound by a nuclear envelope. The surrounding cytoplasm contains many different
membranous organelles. These types of cells are called eukaryotic cells (literally
meaning ‘good nucleus’) – the animal and plant cells in Figure 1.22 (page 21) are
examples.
On the other hand, bacteria contain no true nucleus but have a single, circular
chromosome in the cytoplasm. Also, their cytoplasm does not have the membrane-
bound organelles of eukaryotes. These are called prokaryotic cells (from pro meaning
‘before’ and karyon meaning ‘nucleus’).
Another key difference between the cells of the prokaryotes and eukaryotes is their
size. Prokaryote cells are exceedingly small, about the size of organelles such as the
mitochondria and chloroplasts of eukaryotic cells.
Prokaryotic cell structure

Escherichia coli (Figure 1.24, overleaf) is a bacterium of the human gut – it occurs in
huge numbers in the lower intestine of humans and other endothermic (once known as
‘warm blooded’) vertebrates, such as the mammals, and it is a major component of their
faeces. This tiny organism was named by a bacteriologist, Professor T. Escherich, in
1885. Notice the scale bar in Figure 1.24. This bacterium is typically about 1 μm × 3 μm
in length – about the size of a mitochondrion in a eukaryotic cell. The cytoplasm lacks
the range of organelles found in eukaryotic cells, and a nucleus surrounded by a double
membrane is absent too. The DNA of the single, circular chromosome lacks proteins,
and so is described as ‘naked’. In Figure 1.24 the labels of the component structures are
annotated with their function.
We should also note that all prokaryote cells are capable of extremely rapid growth
when conditions are favourable for them. In such environments, prokaryote cells
frequently divide into two cells (known as binary fission). New cells formed then grow
to full size and divide again.
23
482876_01_Biology_001-030.indd 23 20/02/20 12:55 PM

*structures that occur
1μm
in all bacteria
1 scale bar
flagella – bring about
movement of the
bacterium
pili – enable
attachment to surfaces
and to other bacteria
cytoplasm*– plasma membrane*–

1 Cell structure
site of the chemical a barrier across which

reactions of life all nutrients and waste
products must pass
ribosomes*– site of
protein synthesis
nucleoid*– genetic
material: a single
circular chromosome
of about 4000 genes
mesosome
cell wall*– protects

cell from rupture
caused by osmosis and
possible harm from
food granule plasmid other organisms
electron micrograph of Escherichia coli
▲ Figure 1.24 The structure of Escherichia coli
In summary, the key structural features of typical prokaryotic cells as seen in a typical
bacterium are:
» they are unicellular
» typically 1–5 μm in diameter
» cell walls made of peptidoglycan, composed of polysaccharides and peptides
combined together
» have a single circular chromosome that is ‘naked’ (of DNA without associated proteins)
» ribosomes are present, but they are the smaller 70S variety
» lack organelles surrounded by a double membrane in their cytoplasm.
▼ Table 1.3 Prokaryotes

Prokaryotic and eukaryotic cells compared
and eukaryotes The fundamental differences in size and complexity of prokaryotic and eukaryotic cells
compared are highlighted in Table 1.3.
Prokaryotes, e.g. bacteria, cyanobacteria Eukaryotes, e.g. mammals, green plants, fungi
Cells are extremely small, typically about 1–5 µm in diameter Cells are larger, typically 50–150 µm
Nucleus absent: circular DNA helix in the cytoplasm, DNA Nucleus has distinct nuclear envelope (with pores), with
not supported by histone protein chromosomes of linear DNA helix supported by histone protein
Cell wall present (made of peptidoglycan – long molecules Cell wall present in plants (largely of cellulose) and fungi
of amino acids and sugars) (largely of the polysaccharide chitin)
Few organelles; membranous structures absent Many organelles bounded by double membrane (e.g.
chloroplasts, mitochondria, nucleus) or single membrane (e.g.
Golgi apparatus, lysosomes, vacuoles, endoplasmic reticulum)
Proteins synthesised in small ribosomes (70S) Proteins synthesised in large ribosomes (80S)
Some cells have simple flagella Some cells have cilia or flagella, 200 nm in diameter
Some can fix atmospheric nitrogen gas for use in the None can metabolise atmospheric nitrogen gas but instead
production of amino acids for protein synthesis require nitrogen already combined in molecules in order to
make proteins from amino acids (page 130)
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482876_01_Biology_001-030.indd 24 25/02/20 1:08 PM

always found sometimes present
cell wall
pili
1
cell surface
membrane capsule (polysaccharide
coat) as additional
cytoplasm protection

plasmid
DNA ring
food store infolded cell membrane,

e.g. associated with
photosynthetic pigments,
or particular enzymes
small ribosomes
flagellum
(simple structure)
▲ Figure 1.25 The structure of a bacterium
Question 13 Distinguish between the following terms:

a cell wall and cell surface membrane
b chromatin and chromosome
c nucleus and nucleolus
d prokaryote and eukaryote
e centriole and chloroplast
f plant cell and animal cell.
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482876_01_Biology_001-030.indd 25 20/02/20 12:56 PM

EXTENSION
1
A possible origin for mitochondria and chloroplasts
Present-day prokaryotes are similar to many fossil prokaryotes. Some of these are
3500 million years old. By comparison, the earliest eukaryote cells date back only
1000 million years. Thus eukaryotes must have evolved surrounded by prokaryotes,
many that were long-established organisms. How the eukaryotic cell arose is
not known. However, there is evidence that the origin of the mitochondria and
chloroplasts of eukaryotic cells was as previously independent-living prokaryotes.
1 Cell structure
It is highly possible that, in the evolution of the eukaryotic cell, prokaryotic cells
(which at one stage were taken up into food vacuoles for digestion) came to survive
as organelles inside the host cell, rather than becoming food items! If so, they have
become integrated into the biochemistry of their ‘host’ cell, with time.
The evidence for this origin is that mitochondria and chloroplasts contain:
» a ring of DNA, like the circular chromosome a bacterial cell contains
» small (70S) ribosomes, like those of prokaryotes.
The present-day DNA and ribosomes of these organelles still function with roles in
the synthesis of specific proteins, but the mitochondria and chloroplasts themselves
are no longer capable of living independently.
It is these features that have led evolutionary biologists to propose this
endosymbiotic theory of the origin of these organelles (endo = inside, symbiont =
an organism living with another for mutual benefit).
Viruses as non-cellular structures

Viruses are disease-causing agents, rather than ‘organisms’. The distinctive features of
viruses are:
» they are not cellular structures, but rather consist of a core of nucleic acid (DNA or
RNA) surrounded by a protein coat, called a capsid
» in some viruses there is an additional external envelope or phospholipid membrane
(e.g. HIV)
» they are extremely small when compared with bacteria. Most viruses are in a size
range of 20–400 nm (0.02–0.4 mm). They are visible only by means of the electron
microscope
» they can reproduce only inside specific living cells, so viruses function as
endoparasites in their host organism
» they have to be transported in some way between host cells
» viruses are highly specific to particular host species: some to plant species, some to
animal species and some to bacteria
» viruses are classified by the type of nucleic acid they contain.
DNA viruses RNA viruses
1 single-stranded: 2 double-stranded: 1 single-stranded: 2 double-stranded:
‘M13’ virus of herpes simplex virus poliovirus reovirus of
bacterial hosts of animal hosts of animal hosts animal hosts
size: 25 nm
human size: 80 nm
immunodeficiency
virus, HIV (retrovirus)
size: 500 nm size: 200 nm
size: 100 nm
▲ Figure 1.26 A classification of viruses

26
482876_01_Biology_001-030.indd 26 20/02/20 12:56 PM

enlarged drawing of part of the virus
end view of virus

side view shows hollow
tube construction
position
1
of RNA
protein coat (capsid) of
polypeptide building blocks
arranged in a spiral around
3’ the canal containing RNA

transmission electron micrograph of TMV (×40 000) negatively stained
5’ arrangement of single
strand of RNA in TMV
healthy infected
leaves leaf
▲ Figure 1.27 Tobacco mosaic virus
So are viruses ‘living’ at any stage?

Viruses are an assembly of complex molecules, rather than a form of life. Isolated from
their host cell they are inactive, and are often described as ‘crystalline’. However, within
susceptible host cells they are highly active ‘genetic programmes’ that will take over the
biochemical machinery of host cells. Their component chemicals are synthesised, and
then assembled to form new viruses. On breakdown (lysis) of the host cell, viruses are
released and may cause fresh infections. So, viruses are not living organisms, but may
become active components of host cells.
Relative sizes of molecules, macromolecules, viruses and

organisms
We now have a clear picture of prokaryotic and eukaryotic levels of cellular organisation
and of the nature of viruses. Finally, we ought to reflect on the huge differences in size
among organisms, viruses and the molecules they are built from.
In Figure 1.28 (overleaf) size relationships of the biological and chemical levels of
organisation on which we focus in this book are compared. Here the scale is logarithmic
to accommodate the diversities in size in the space available. So each division is ten
times larger than the division immediately below it. (In science, ‘powers to ten’ are used
to avoid writing long strings of zeros.) Of course we must remember that, although
sizes are expressed by a single length or diameter, all cells and organisms are three-
dimensional structures, with length, breadth and depth.
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482876_01_Biology_001-030.indd 27 20/02/20 12:56 PM

1
Log Object Methods of Name of study
scale observation or approach
(m) with their limit
102 100 m redwood tree
Morphology
1 Cell structure
101 length of whale study of visible

form – external
structure
human height
100 1m
Anatomy
study of
human eye the internal
10–1
organisation
of living things
10–2
simple
cross-section of
microscope
giant nerve cell
(hand lens)
of squid
10–3 1 mm
Histology
study of tissues
–4
10
range of
diameters Cytology
microscope study of cells
of most (high power)
10–5 eukaryotic
cells
organelles
prokaryotic
cells Ultra-structure
10–6 1 µm
electron study of organelles
microscope and membranes
10–7
viruses
10 –8
thickness of (sizes vary)
cell membranes Molecular
structure
smaller macromolecules and
10–9 1 nm
no method Atomic
small amino acid of observation structure
by chemical analysis
10–10
hydrogen atom
10–11
▲ Figure 1.28 Size relationships on a logarithmic scale
28
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SUMMARY
» Cells are the building blocks of living things. and they have a true nucleus. These living things
1
They are derived from other cells by division and are called eukaryotes.
they are the site of all the chemical reactions of » Examination of transmission electron
life (metabolism). A cell is the smallest unit of micrographs has revealed that the cytoplasm of
organisation we can say is alive. the eukaryotic cell contains numerous organelles,
» Cells are extremely small. They are measured some about the size of bacteria, suspended in an
in units of a thousandths of a millimetre (a aquatic solution of metabolites (called the cytosol)
End of topic questions

micrometre – µm) and they must be viewed by surrounded by the cell surface membrane.
microscopy. In the laboratory we view them by » Many of the organelles are membrane-bound
light microscopy using a compound microscope. structures, including the nucleus, mitochondria,
» The cells of plants and animals have common chloroplasts, endoplasmic reticulum, Golgi
features, including a nucleus, cytoplasm and apparatus and lysosomes. The organelles have
cell membrane. To observe and resolve the specific roles in metabolism. The biochemical
detailed structures within the cytoplasm, roles of the organelles are investigated by
electron microscopy is required. The distinctive disrupting cells and isolating the organelles for
features of plant cells are a cellulose cell wall, further investigation.
the presence of large permanent vacuoles and » Viruses are non-cellular structures that consist of
the possible presence of chloroplasts, the site of a core of nucleic acid (DNA or RNA) surrounded by
photosynthesis. a protein coat, called a capsid. They are extremely
» The simplest cellular organisation is shown by small when compared with bacteria, and they
bacteria. Here there is no true nucleus. These can reproduce only inside specific living cells, so
unicellular organisms are called prokaryotes. viruses function as endoparasites in their host
The cells of plants, animals and fungi are larger organism.

e Which of the organelles of the cell are surrounded by a double membrane? [3]
lysosomes and say why. [4]
[Total: 20]
2 By means of fully annotated diagrams only:
a Illustrate the general structure of a eukaryotic animal cell as seen by
electron microscopy.
b Outline how this cell carries out:
i the packaging and export of polypeptides
ii the destruction of defective organelles.
29
482876_01_Biology_001-030.indd 29 20/02/20 12:56 PM

3 a T
he discovery that bacteria have a different level of cell organisation
from the cells of animals and plants awaited the application of electron
1 microscopy in biology. Why was this the case?
b Explain what the terms ‘prokaryote’ and ‘eukaryote’ tell us about
[2]
the respective structures of cells of these organisms. [2]

c Make a large, fully labelled diagram of a prokaryotic cell. [6]
d Describe five ways in which prokaryotic cells differ from animal
and plant cells. [10]
[Total: 20]
4 a What features of cells are observed by electron microscopy that are
1 Cell structure
not visible by light microscopy? [1]

b i What magnification occurs in a light microscope with a ×6 eyepiece
lens and a ×10 objective lens? [1]
ii How many cells of 100 μm diameter will fit side by side along a millimetre? [1]
iii Explain what is meant by the resolution (resolving power) of a microscope.[2]
[Total: 5]
30
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AS LEVEL
2.1 Testing for biological molecules

This topic introduces Learning outcomes
carbohydrates, lipids and
proteins: organic molecules
that are important in cells. 2.1.1 describe and carry out the Benedict’s test for reducing sugars, the iodine
Nucleic acids, another class test for starch, the emulsion test for lipids and the biuret test for proteins
of biological molecule, are 2.1.2 describe and carry out a semi-quantitative Benedict’s test on a reducing
covered in Topic 6. All of sugar solution by standardising the test and using the results (time to
these molecules are based first colour change or comparison to colour standards) to estimate the
on the versatile element concentration
carbon. This topic explains
2.1.3 describe and carry out a test to identify the presence of non-reducing
how carbohydrates, lipids
and proteins, which have a sugars, using acid hydrolysis and Benedict’s solution
great diversity of function
in organisms, are assembled
from smaller organic Starting point
molecules such as glucose, ★ Tests for biological molecules can be used in a variety of contexts, such as
amino acids, glycerol and
identifying the contents of mixtures of molecules and following the activity of
fatty acids.
digestive enzymes.
The emphasis in this topic is
on the relationship between
molecular structures and
their functions. Some of 2.1 Testing for biological molecules
these ideas are continued
in other topics, for
example, the functions
Introducing the tests for biological molecules
of haemoglobin in gas The methods you will use to test for biological molecules are summarised in Figure 2.1.
transport in Transport Each test exploits the chemical structure and properties of the groups of molecules it
in mammals (Topic 8), is designed to detect. Consequently, details of the tests are described in that context,
phospholipids in membranes later in Section 2.2 (for reducing sugars, non-reducing sugars, starch, and lipids)
in Cell membranes and and in Section 2.3 (for proteins). Most tests are used to detect the presence or absence
transport (Topic 4) and
of particular molecules. The test for reducing sugar can be adapted to estimate
antibodies in Immunity
(Topic 11). concentration, and may be used in experiments that follow the activity of a digestive
enzyme, for example – as explained on page 34.
Life as we know it would
not be possible without
water. Understanding Testing for reducing sugars
the properties of this This reaction is used to test for reducing sugar and is known as Benedict’s test (Figure 2.2).
extraordinary molecule is an If no reducing sugar is present the solution remains blue.
essential part of any study
of biological molecules.
Some of the roles of water
Steps to the Benedict’s test
are in this topic, others are 1 Heat a water bath (large beaker) of water to 100 °C. Since this takes some time, set it
in Topics 4, 7, 8, 12, 13 up before you begin preparing for the testing.
and 14. 2 From a 10% solution of glucose (18.0 g of glucose with 100 cm3 of distilled water):
– prepare 10 cm3 of a 0.1% solution of glucose (labelled Tube 2)
– prepare 10 cm3 of a 1% solution of glucose (Tube 3)
– and then place 10 cm3 of the 10% glucose solution in another test tube (Tube 4).
3 Finally, place 10 cm3 of distilled water in a test tube (Tube 1) and 10 cm3 of a 10%
sucrose solution in a final test tube (Tube 5).
31
482876_02_Biology_031-060.indd 31 20/02/20 12:56 PM

Start
2 lipid (fat + oil)

What do you
want to test
protein
starch for? non-reducing sugars
see see see see

page 33 page 33 reducing sugars page 35 pages 33–4
see add 1 cm3 add 1 cm3

add 2 cm3 add a few drops pages 31–2 hydrochloric sodium
ethanol of I2KI (iodine)
acid hydroxide
add an equal
quantity of put test tube in add 5 drops of

shake Benedict’s a boiling water copper sulfate
solution bath for 3 min to produce
Does it turn
blue/black? a colour
put test tube
allow to settle yes no in boiling water
in test tube rack cool
for 3 min
for 2 min
no What is the
starch colour of
starch
present the solution?
decant off clear present What add solid
liquid into a test colour is sodium
pink,
tube of 2 cm3 the solution hydrogen- pale
after being carbonate until lilac,
distilled water blue
boiled? it stops fizzing purple
yellow,
green, no
brown, blue soluble
soluble
orange, protein
Is the liquid protein
red present
cloudy? present
yes no
no
sugars Risk assessments:
sugars
lipids no present Eye protection is essential when heating water and solutions.
present
are lipids Otherwise, good laboratory practice is sufficient to take account
present present of any hazards and avoid significant risk.
▲ Figure 2.1 Flow chart of the tests for biological molecules
4 Add 5 cm3 of Benedict’s solution to each tube.

5 Place all five tubes in the water bath for 5 minutes, gently agitating them during
the process. Finally, remove the tubes to a rack where any colour changes can be
observed (Figure 2.2).
Notice that:
– in the absence of reducing sugar the solution remains blue (Tube 1)
– sucrose is not a reducing sugar (Tube 5)
– in the presence of glucose, the colour change observed depends on the
concentration of reducing sugar. The greater the concentration the more
precipitate is formed, and the greater the colour changes:
blue → green → yellow → red → brown
5 cm3 of Benedict’s solution test tubes were placed in a boiling tubes were transferred to a rack and the
(blue) was added to 10 cm3 water bath for 5 minutes colours compared
of solution to be tested
1 2 3 4 5
boiling
water bath
with distilled with sucrose
water solution
(control)
with 0.1% with 1.0% with 10%

glucose solution glucose solution glucose solution
▲ Figure 2.2 The test for reducing sugar

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Testing for starch
We test for starch by adding a solution of iodine in potassium iodide. A blue–black
colour indicates the presence of starch (Figure 2.3). 2
test for starch with iodine in potassium iodide solution; the blue–black colour comes from a starch/iodine complex
2.1 Testing for biological molecules

1% starch 0.1% starch 0.01% starch
solution solution solution
a) Test on a potato tuber cut surface b) Test on starch solutions of a range of concentrations
▲ Figure 2.3 Testing for starch with iodine in potassium iodide solution
The emulsion test for lipid

When organic matter is shaken up with a small quantity of absolute ethanol, if lipid
is present it will become dissolved in this organic solvent (see Figure 2.4). Then,
when an equal quantity of cold water is added, a cloudy white suspension will form,
since lipid is totally immiscible with water. Alternatively, in the absence of lipid
in the original material, alcohol and water will mix and the resulting solution will
remain transparent.
oil forms a layer on water, but when shaken together, froms an

emulsion (milky in appearance) which may take a while to disperse
▲ Figure 2.4 The emulsion test
Testing for proteins

The biuret test is used as an indicator of the presence of protein because it gives a
purple colour in the presence of peptide bonds (–C– N–). To a protein solution, an
equal quantity of sodium hydroxide solution is added and mixed. Then a few drops
of 0.5 per cent copper(ii) sulfate is introduced with gentle mixing. A distinctive
purple colour develops without heating (see Figure 2.5, overleaf).
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482876_02_Biology_031-060.indd 33 20/02/20 12:56 PM

egg white wheat flour 1% starch
to the solution to be tested add: solution solution solution (control)
2 2M sodium hydroxide solution
then:
0.5% copper(II) sulfate
solution (via dropping bottle)
purple colour remains

develops blue
▲ Figure 2.5 The biuret test for protein
Making the Benedict’s test semi-quantitative

The colour sequence obtained with Benedict’s solution with sugar solutions of increasing
concentration can be used to make an approximate estimation of the concentration
of reducing sugar in other solutions of unknown concentration. To discover the
relationship between colour and concentration, accurate quantities need to be used. The
steps to using Benedicts test semi-quantitatively are shown in Figure 2.6.
making a serial dilution of glucose solution

Benedict’s test
3 add 2 cm3 1% glucose to tube 2,
8 add 2 cm3 Benedict’s solution to
mix thoroughly
each tube and mix thoroughly
4 transfer 2 cm3 of this 5 repeat this serial dilution

solution to tube 3 with tubes 4, 5 and 6 5
3
7 place all tubes in a boiling 1 2 4
1 add 2 cm3 1% glucose
solution to tube 1 2 cm3 2 cm3 water bath for 3 minutes
6 discard 2 cm3
of the solution in tube 6
1 2 3 4 5 6
2 add 2 cm3 water to tubes 2–6
9 return the tubes to the test-tube rack and note the colours
▲ Figure 2.6 Using the Benedict’s test semi-quantitatively
Look at the sequence of actions carefully. Note that the product of steps 1–6 is a serial
dilution of glucose starting with 1% glucose. Each subsequent dilution is 50% less
concentrated.
What is the concentration of the glucose solution in Tube 6?
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Steps 7 and 8 are the Benedict’s tests, carried out on each tube. The tubes are held in the
boiling water for a standard length of time, at least 3 minutes, before being removed and
the colour recorded. The colour produced by an unknown glucose solution, tested with
Benedict’s in the same way, indicates the concentration of glucose present.
2
Testing for non-reducing sugars
To demonstrate that sucrose is a non-reducing sugar, two tests are required. To carry
these out:
1 Dissolve a small spatula-load of sucrose in half a test tube of distilled water, and split
2.2 Carbohydrates and lipids

the resulting solution equally between two test tubes, labelled A and B.
2 To A, add approximately 1 cm3 of dilute hydrochloric acid, and to B add the same
quantity of distilled water. Heat both tubes in a boiling water bath for 1 minute.
3 Remove both tubes and cool to room temperature. To tube A, cautiously add a small
quantity of sodium hydrogencarbonate powder to neutralise any excess acid. When
no more effervescence occurs on addition of the powder, all the acid will have been
neutralised, and conditions will now be alkaline in the tube.
4 Add a small quantity of Benedict’s solution to each tube and heat for a standard time
in the water bath. Then remove the tubes and compare the final colours.
5 In tube A the sucrose will have been hydrolysed (by acid, in this case) to glucose and
fructose, and these reducing sugars with give a positive result in the Benedict’s test.
In tube B the sucrose present will have caused no colour change, but Tube B has
established the initial absence of reducing sugar.

Learning outcomes
2.2.1 describe and draw the ring forms of α-glucose and β-glucose
2.2.2 define the terms monomer, polymer, macromolecule, monosaccharide,
disaccharide and polysaccharide
2.2.3 state the role of covalent bonds in joining smaller molecules together to
form polymers
2.2.4 state that glucose, fructose and maltose are reducing sugars and that
sucrose is a non-reducing sugar
2.2.5 describe the formation of a glycosidic bond by condensation, with
reference to disaccharides, including sucrose, and polysaccharides
2.2.6 describe the breakage of a glycosidic bond in polysaccharides and
disaccharides by hydrolysis, with reference to the non-reducing sugar test
2.2.7 describe the molecular structure of the polysaccharides starch (amylose
and amylopectin) and glycogen and relate their structures to their
functions in living organisms
2.2.8 describe the molecular structure of the polysaccharide cellulose and
outline how the arrangement of cellulose molecules contributes to the
function of plant cell walls
2.2.9 state that triglycerides are non-polar hydrophobic molecules and describe
the molecular structure of triglycerides with reference to fatty acids
(saturated and unsaturated), glycerol and the formation of ester bonds
2.2.10 relate the molecular structure of triglycerides to their functions in living
organisms
2.2.11 describe the molecular structure of phospholipids with reference to
their hydrophilic (polar) phosphate heads and hydrophobic (non-polar)
fatty acid tails
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Starting point
2 ★ Carbohydrates and lipids have important roles in the provision and storage of
energy and for a variety of other functions such as providing barriers around
cells: the phospholipid bilayer of all cell membranes and the cellulose cell
walls of plant cells.
Compounds built from carbon and hydrogen are called organic compounds.
Question Examples include methane (CH4) and glucose (C6H12O6). Carbon is not a common
1 Where do non- element of the Earth’s crust – it is quite rare compared to silicon and aluminium, for
organic forms of example. But in living things carbon is the third most abundant element by mass, after
carbon exist in the oxygen. In fact, organic compounds make up the largest number of molecules found
biosphere? in living things. This includes the carbohydrates, lipids and proteins.
Why is carbon so important to life?
The answer is that carbon has a unique collection of properties, so remarkable in fact,
that we can say that they make life possible.
Carbohydrates
Carbohydrates are the largest group of organic compounds. They include sugars, starch,
glycogen and cellulose. Carbohydrates are substances that contain only three elements:
carbon, hydrogen and oxygen. The hydrogen and oxygen atoms are present in the
ratio 2:1 (as they are in water, H 2O). In fact, we represent carbohydrates by the general
formula Cx(H2O)y.
We start by looking at the simplest carbohydrates.
Monosaccharides – the simple sugars

Monosaccharides are carbohydrates with relatively small molecules. They taste sweet
and they are soluble in water. In biology, the monosaccharide glucose is especially
important. All green leaves manufacture glucose using light energy, our bodies transport
glucose in the blood and all cells use glucose in respiration. In cells and organisms
glucose is the building block for many larger molecules, including cellulose.
The structure of glucose

Glucose has a chemical or molecular formula of C6H12O6. This indicates the atoms
present and their numbers in the molecule. So, glucose is a six-carbon sugar or hexose.
But this molecular formula does not tell us the structure of the molecule.
Glucose can be written down on paper as a linear molecule however it cannot exist
in this form. Rather, glucose is folded and takes a ring or cyclic form. This is its
structural formula. The ring closes up when the oxygen on carbon-5 attaches itself to
carbon-1. The glucose ring, containing five carbon atoms and an oxygen atom, is called
a pyranose ring. Furthermore, the pyranose ring exists in two forms. These are the
a-form and the b-form, depending on whether a –H atom was trapped ‘up’ (α -form)
or ‘down’ (b-form) when the ring closed. So, there are two forms of glucose, known as
a-glucose and b-glucose (Figure 2.7).
Incidentally, fructose is another hexose sugar found in cells. It has a ring structure
different from that of glucose. Fructose forms into a ring with four carbon atoms and
an oxygen atom (known as furanose ring). Fructose is by far the sweetest common
sugar; fructose is used in the food industry in the manufacture of sweets and various
confectioneries.
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OH
6
2
H C H
Glucose exists in two ring forms. H 5
In solution, glucose molecules C OH
constantly change between the two H
O glucose, folded
4
ring structures. C OH H 1C
3 2
C C H
OH
H OH
CH2OH 6
CH2OH
6

H 5C O H H 5C O OH
H glucose in H
4C
OH H 1C 4 C OH H 1C
pyranose rings
OH C C OH the two forms of glucose OH C C H
3 2 3 2
`-glucose H OH depend on the positions of H OH
the —H and —OH attached a-glucose
to carbon-1 when the ring closes
6 6
CH2OH CH2OH
5 O H 5
For simplicity and convenience O OH
4 OH C1 it is the skeletal formulae that 4 OH C1
3 2 3 2
OH are most frequently used in H
OH recording biochemical reactions OH
OH OH
and showing the structure of
skeletal formula biologically active molecules skeletal formula
of α-glucose of β-glucose
▲ Figure 2.7 The structure of a-glucose and b-glucose
Other monosaccharides of importance in living cells

There are several other sugars produced by cells and used in their chemical
reactions. These include some three-carbon sugars (trioses) that are early products in
photosynthesis in green plants (Topic 13). Five-carbon sugars (pentoses) are important
components of nucleic acids (Topic 6).
Length of Molecular
carbon chain Name of sugar formula Formula Roles
3C 5 triose glyceraldehyde C3H6O3 H O intermediate in
C
respiration and
H C OH
photosynthesis
CH 2OH
5C 5 ribose C5H10O5 H O in RNA, ATP

C CH 2OH OH
pentoses O and hydrogen
H C OH
acceptors NAD
H C OH and NADP
H C OH
HO OH
CH 2OH
Question deoxyribose C5H10O4 H

C
O
CH 2OH OH
in DNA
O
2 List the properties H C H
of the carbon atom H C OH
responsible for the H C OH
huge array of organic HO
CH 2OH
compounds.
▲ Table 2.1 Other monosaccharides of importance in living cells
Disaccharides
Disaccharides are carbohydrates made of two monosaccharides combined together. An
example is sucrose. Sucrose is formed from a molecule of a-glucose and a molecule of
fructose.
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EXTENSION
2 The functional groups of sugars
Fortunately, the huge number of organic compounds fit into a relatively small number of ‘families’ of compounds.
These families are identified by a part of their molecule that is the functional group. It is the functional group of
an organic compound that gives it characteristic chemical properties. The chemical structures of some important
functional groups are shown in Figure 2.8.
Some functional Other functional

groups of sugars groups H

amino group N
H
H
CH2OH alcohol group C O H
H C O H hydroxyl group OH
aldehyde
H H
C OH H C functional O
group C sulfydryl group S H
OH C C OH carboxyl group COOH or C
O H
α-glucose H OH (or ––CHO) O H
an aldose O
carbonyl group C O (this group is part of phosphate group O P O H

the aldehyde, keto O
and carboxyl groups)
▲ Figure 2.8 Some functional groups

The remainder of the organic molecule, referred to as the R-group, has little or no effect on the chemical properties
of the functional group. However, the R-group does influence the physical properties of the molecule. These
include whether a compound is a solid or liquid (its melting point) and at what temperature a liquid becomes
vapour (its boiling point).
All the monosaccharides contain one of two functional groups. Some are aldehydes, like glucose, and are referred
to as aldo-sugars or aldoses. Others are ketones, like fructose, and are referred to as keto-sugars or ketoses.
Aldoses and ketoses are reducing sugars. This means that, when heated with an alkaline solution of copper(ii)
sulfate (a blue solution, called Benedict’s solution), the aldehyde or ketone group reduces Cu21 ions to Cu1 ions
forming a brick-red precipitate of copper(i) oxide. In the process, the aldehyde or ketone group is oxidised to a
carboxyl group (–COOH). The test for reducing sugars is outlined on pages 31–32.
Sucrose and fructose are both reducing sugars.
Condensation and hydrolysis reactions

A molecule of water is removed when two monosaccharides combine, so the reaction is
called a condensation reaction. The bond formed between the a-glucose and fructose
molecules by the removal of water is called a glycosidic bond (Figure 2.9). This is
another example of a strong, covalent bond.
Figure 2.9 Sucrose (a sucrose α-glucose fructose

▲
+
disaccharide) and the CH2OH
monosaccharides that
O glycosidic
form it CH2OH
bond
1 CH2OH HO CH2OH
OH O
O O O
HO hydrolysis
2 + H2O +
HO condensation OH HO
water
HO HOH2C HOH2C
HO OH
OH HO OH
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482876_02_Biology_031-060.indd 38 20/02/20 12:57 PM

In the reverse process, a disaccharide is ‘digested’ to the component monosaccharides in
a hydrolysis reaction. This reaction involves adding a molecule of water (‘hydro-’) at the
Question same time as the splitting (‘-lysis’) of the glycosidic bond occurs (Figure 2.9). 2
3 What is meant by Sucrose is not a reducing sugar. This is because the aldehyde group of glucose and the
a a non-reducing ketone group of fructose (which are reducing groups) are used to form the glycosidic bond
sugar in sucrose. Neither is then available to reduce copper(ii) to copper(i) in a Benedict’s test.
Benedict’s solution will remain blue when heated with sucrose. The test for non-reducing
b a glycosidic bond?
sugars is outlined on page 35.

Sucrose and other disaccharides
Sucrose is an important sugar. It is sucrose that is transported from leaves to the
growing points of plant stems and roots or to the carbohydrate storage sites all over the
plant. This occurs in the sieve tubes of phloem tissue. Sucrose is also the ‘sugar’ humans
mostly prefer to use in foods and drinks. The sugar industry extracts and purifies
sucrose from sugar beet and sugar cane.
There are other disaccharides formed in cells, depending on which monosaccharides are
involved and whether they are in their a or b condition. Two other commonly occurring
disaccharides are maltose and lactose.
Maltose (a-glucose 1 a-glucose) is a product of starch hydrolysis. The extraction of
maltose from germinating barley (as malt extract) is an important industry. Malt is used
in brewing and in food manufacture.
Lactose (b-galactose 1 glucose) is the sugar found in the milk of mammals.
Maltose and lactose are both reducing sugars.
Finally, a definition check:
» Monosaccharides are simple sugars; all are reducing sugars.
» Disaccharides are sugars that are condensation products of two monosaccharide
molecules, with the elimination of water and the formation of a glycosidic bond.
Some disaccharides are reducing sugars and some are non-reducing sugars.
Polysaccharides
Polysaccharides are built from very many monosaccharide molecules condensed
together. Once they are part of a larger molecule, they are called residues. Each residue
is linked by glycosidic bonds. ‘Poly’ means ‘many’ and, in fact, thousands of ‘saccharide’
residues make up a polysaccharide. So a polysaccharide is an example of a giant
molecule, a macromolecule. Normally each polysaccharide contains only one type of
monomer. Cellulose is a good example – built from the monomer glucose.
Bonds in polysaccharides
Atoms naturally combine together (they ‘bond’) to form molecules in ways that
have a stable arrangement of electrons in the outer shells of each atom. In covalent
bonding, electrons are shared between atoms. Covalent bonds are the strongest bonds
in biological molecules. In polysaccharides, the individual monomers are held by
covalent bonds.
However, entirely different bonds, called hydrogen bonds, are also formed. We can
illustrate how hydrogen bonds form by reference to the water molecule.
Water is composed of one atom of oxygen and two atoms of hydrogen, also combined by
covalent bonding. The water molecule is triangular rather than linear, and the nucleus
of the oxygen atom draws electrons (negatively charged) away from the hydrogen
nuclei (positively charged) – with an interesting consequence. Although overall the
water molecule is electrically neutral, there is a net negative charge on the oxygen atom
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(conventionally represented by Greek letter delta as δ−) and a net positive charge on
the hydrogen atoms (represented by δ+). In other words, the water molecule carries an
2 unequal distribution of electrical charge within it. This unequal distribution of charge
is called a dipole. Molecules that contain groups with dipoles are known as polar
molecules. Water is a polar molecule (see Figure 2.27, page 56).
Dipoles exist in many different molecules, especially where there are -OH, -C=O, or
=N–H groups, so hydrogen bonds can form between these groups. Hydrogen bonds
are weaker than covalent bonds, but never the less are very important in the structure
and properties of carbohydrates (including polysaccharides) and proteins. For example,
molecules containing these groups are attracted to water molecules because of their
dipoles, and are therefore said to be ‘water loving’ or hydrophilic.
Starch
Starch is a mixture of two polysaccharides (Figure 2.10).
» Amylose is an unbranched chain of several thousand 1,4 linked a-glucose units.
» Amylopectin has shorter chains of 1,4 linked a-glucose units but, in addition, there
are branch points of 1,6 links along its chains.
Question These covalent bonds between glucose residues in starch bring the molecules together as
a helix. The whole starch molecule is stabilised by countless hydrogen bonds between
4 Starch is a powdery parts of the component glucose molecules.
material; cellulose
is a strong, fibrous Starch is the major storage carbohydrate of most plants. Starch is an important energy
substance; yet both source in the diet of many animals, too. Its usefulness lies in the compactness and
are made of glucose. insolubility of its molecule. However, it is readily hydrolysed to form sugar when
What features of the required. We sometimes see ‘soluble starch’ as an ingredient of manufactured foods.
cellulose molecule Here the starch molecules have been broken down into short lengths, making them
account for its more easily dissolved.
strength?
The test for starch is described on page 33.
CH 2OH CH 2OH CH 2OH CH 2OH

O O O O
amylose
(a straight-chain OH OH OH OH
polymer of α-glucose) O O O O O
OH OH OH OH
α-1,4-glycosidic bonds
CH 2OH CH 2OH
O O
OH OH
O O
OH HO
O α-1,6-glycosidic bond
amylopectin
(a branched-chain CH 2OH CH 2OH CH 2 CH 2OH
polymer of O O O O
α-glucose)
OH OH OH OH
O O O O O
OH OH OH OH
▲ Figure 2.10 Starch
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482876_02_Biology_031-060.indd 40 20/02/20 12:57 PM

Structural formula residue at
branch point
HOCH2
H O H
HOCH2
H O H
HOCH2
H O H
α-1,6 linkage
between two
2
glucose residues
H H H
OH H OH H OH H
residues at the HO O O O
end of chains
H OH H OH H OH
HOCH2 HOCH2 HOCH2 HOCH2 HOCH2 CH2 HOCH2

H O H H O H H O H H O H H O H H O H H O H
H H H H H H H
OH H OH H OH H OH H OH H OH H OH H
HO O O O O O O R
H OH H OH H OH H OH H OH H OH H OH
α-1,4 linkage
between two
glucose residues
▲ Figure 2.11 Glycogen
TEM of a liver cell (×7000)

Glycogen
Glycogen is a polymer of a-glucose, chemically very
similar to amylopectin, although larger and more highly
branched (Figure 2.11). Glycogen is one of our body’s
energy reserves and is drawn upon and respired as
needed. Granules of glycogen are seen in liver cells
(Figure 2.12), muscle fibres, and throughout the tissues
of the human body. The one exception is in the cells of
the brain. Here virtually no energy reserves are stored.
Instead brain cells require a constant supply of glucose
from the blood circulation.
Cellulose
Cellulose is by far the most abundant carbohydrate – it
makes up more than 50 per cent of all organic carbon.
▲ Figure 2.12 Glycogen granules (dark blue spots) in liver (Remember, the gas carbon dioxide, CO2, and the
cells mineral calcium carbonate, CaCO3, are examples of
inorganic carbon.)
Cellulose is a polymer of b-glucose molecules combined together by glycosidic bonds
between carbon-4 of one b-glucose molecule and carbon-1 of the next. Successive
glucose units are linked at 1808 to each other (Figure 2.13, overleaf). This structure is
stabilised and strengthened by hydrogen bonds between adjacent glucose units in the
same strand and, in fibrils of cellulose, by hydrogen bonds between parallel strands, too.
The strength of plant cell walls results from the combined effect of the bonds between
b-glucose monomers, the hydrogen bonds within and between these chains of b-glucose
and the way in which the fibres are arranged in different directions.
Question
Cellulose occurs in the cell walls of green plants and the debris of plants in and on
5 Define the terms the soil. It is an extremely strong material – insoluble, tough and durable but slightly
‘monomer’ and elastic. Cellulose fibres are straight and uncoiled. When it is extracted from plants,
‘polymer’, giving cellulose has many industrial uses. We use cellulose fibres as cotton, we manufacture
examples from the
them into paper, rayon fibres for clothes manufacture, nitrocellulose for explosives,
carbohydrates.
cellulose acetate for fibres of multiple uses, and cellophane for packaging.
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β-glucose molecules
two β-glucose molecules rotated 180° with
2 and the formation of a

1,4 glycosidic link
respect to the other
CH2OH
the strands are held straight by covalent bonds between
glucose units, and by hydrogen bonds within the strand
H OH
OH C C C O OH
H H CH 2OH H O OH CH 2OH H O OH CH 2OH O OH
OH H H
C carbon-1 C C carbon-4 C O O O O O O
H OH H H
H repeated
C OH OH C C O O
O O O O
×n
CH2OH H OH HO OH H O H OH OH
CH 2OH OH CH 2 CH 2OH
—OH groups react with O

HO OH CH 2OH H O OH CH 2OH
the removal of H2O
O O O
the cellulose fibre is
strengthened by all
O O
these bonds O O
CH 2OH HO OH CH 2OH HO OH
cellulose strands
packed together glucose molecules
to form fibrils form straight,
unbranched chains
fibres of
cellulose laid
down at different
electron micrograph of angles
cellulose in a plant cell wall
(×1500)
▲ Figure 2.13 Cellulose
Other sugar compounds

In addition to cellulose, plant cell walls contain small quantities of substances called
pectins and hemicelluloses. These are mixtures of polysaccharides formed from
organic acids, themselves made from sugars. These ‘acids’ occur as their calcium salts.
For example, we have calcium pectate in plant cell walls. We can think of these pectins
and hemicelluloses as the ‘glues’ that hold the cellulose of cell walls of plants together. At
the junction between walls these substances appear as a layer called the middle lamella.
Pectins and hemicelluloses also pass between the cellulose fibres, adding to the strength
of the cell wall.
Lipids
Lipids contain the elements carbon, hydrogen and oxygen, as do carbohydrates.
However, in lipids the proportion of oxygen is much less. Lipids are insoluble in water.
In fact they generally behave as ‘water-hating’ molecules, a property described as
hydrophobic. Lipids can be dissolved in organic solvents such as alcohol (for example,
ethanol), propanone and ether. This property is made use of in the emulsion test for
lipids (see page 33).
Lipids occur in living things as animal fats and plant oils (Figure 2.14). They are also
present as the phospholipids of cell membranes. In addition, there are other, more
unusual forms of lipid. For example, the steroids from which many growth and sex
hormones are produced are lipids. The waxes found on plants and animals are also lipids.
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2
meat joint with fat layers around olive oil nuts and seeds rich

the blocks of muscle fibres in oils
▲ Figure 2.14 Fats and oils – these all leave a translucent stain on paper or fabric
Fats and oils

Fats and oils are compounds called triglycerides (strictly, triacylglycerols). They are
formed by reactions in which water is removed. These condensation reactions occur
between fatty acids (full name, monocarboxylic acids) and an alcohol called glycerol,
as shown in Figure 2.15, overleaf. Three fatty acid molecules combine with one glycerol
molecule to form a triglyceride. Fats and oils are both formed in this way and they have
the same chemical structure. The only difference between them is that at about 20 8C
(room temperature) oils are liquids and fats are solid.
Triglycerides are quite large molecules but they are small when compared to
macromolecules such as glycogen and starch. It is only because of their non-polar,
hydrophobic properties that triglyceride molecules clump together (aggregate) into huge
globules that make them appear to be macromolecules.
The fatty acids present in fats and oils have long hydrocarbon ‘tails’. These are typically
about 16–18 carbon atoms long but may be anything between 14 and 22 (Figure 2.15).
The hydrophobic properties of triglycerides are due to these hydrocarbon tails.
We describe fatty acid molecules as ‘acids’ because their functional group (–COOH,
carboxyl) tends to ionise (slightly) to produce hydrogen ions, which is the property of
an acid.
−COOH ∆ −COO 2 1 H1
It is the carboxyl functional group of three organic acids that react with the three
hydroxyl functional groups of glycerol to form a triglyceride (Figure 2.15). The bonds
formed in this case are known ester bonds.
Saturated and unsaturated triglycerides

Much attention is paid to the value of ‘unsaturated fats’ in the diet – especially among
people who are overweight. Fats and oils which are saturated have no double bonds
(–C5C–) between the carbon atoms in their hydrocarbon tails, whereas unsaturated
fats and oils have one or more double bonds present in the hydrocarbon tails
(Figure 2.16, page 45).
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The carboxyl group ionises to form O O
hydrogen ions, i.e. it is a weak acid. C C + H+
2 O H O –
hydrocarbon tail carboxyl group H
H H H H H H H O HO C H
H H H H H H H H
HO C H
H C C C C C C C C +
C C C C C C C C
O H HO C H
H H H H H H H
H H H H H H H H
H
the synthesis
this is palmitic acid with 16 carbon atoms involves fatty acids
and glycerol
a bond is formed between the carboxyl group (—COOH) of fatty acid

and one of the hydroxyl groups (—OH) of glycerol, to produce a monoglyceride:
H O H O
H C OH + C (CH2)n CH3 H C O C (CH2)n CH3 + H2O
H C OH OH H C OH with an
H2O ester link
H C OH H C OH
H H
glycerol + fatty acid monoglyceride + water
the process is repeated to give a diglyceride and then a triglyceride is formed

H O H O
H C O C (CH2)nCH3 H C O C (CH2)nCH3
O O
H C O C (CH2)nCH3 H C O C (CH2)nCH3
O
The three fatty acids in a
H C OH H C O C (CH2)nCH3 triglyceride may be all the
same, or may be different.
H H
▲ Figure 2.15 The formation of a triglyceride
Where several double bonds occur the resulting fat is called polyunsaturated. Fats with
unsaturated fatty acids melt at a lower temperature than those with saturated fatty acids,
because their unsaturated hydrocarbon tails do not pack so closely together. You can see
why in Figure 2.16.
This difference between saturated and polyunsaturated fats is important in the manufacture
of margarine and butter spreads, since the later perform better ‘from the fridge’. There is
disagreement about the value (or otherwise) of ‘polyunsaturates’ in the human diet. What
seems clear is that it is better to eat less rather than more fat in our diets.
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palmitic acid, C15H31COOH, a saturated fatty acid oleic acid, C17H33COOH, an unsaturated fatty acid
H H H H H H H H H H H H H H O H H H H H H H H H H H H H H H H O 2
H3C C C C C C C C C C C C C C C C H3C C C C C C C C C C C C C C C C C C
H H H H H H H H H H H H H H O H H H H H H H H H H H H H H H O H
space-filling model space-filling model

O
skeletal formula C OH
O
C skeletal formula
OH
(the double bond causes

a kink in the hydrocarbon
‘tail’)
O O
CH2 O C CH2 O C
O O
CH O C CH O C
O O
CH2 O C CH2 O C
tristearin, melting point 72ºC triolein, melting point –4ºC
▲ Figure 2.16 Saturated and unsaturated fatty acids, and the triglycerides they form
The roles of fats and oils in living things

Energy source and metabolic water source
When triglycerides are oxidised in respiration a lot of energy is transferred to make ATP
(see page 244). Mass for mass, fats and oils release more than twice as much energy as
carbohydrates do when they are respired. This is because fats are more reduced than
carbohydrates (page 244). More of the oxygen in the respiration of fats comes from the
atmosphere. In the oxidation of carbohydrate, more oxygen is present in the carbohydrate
molecule itself. Fat therefore forms a concentrated, insoluble energy store.
Fat layers are typical of animals that endure long unfavourable seasons in which they
survive by using the concentrated reserves of food stored in their bodies. Oils are often a
major energy store in plants, their seeds and fruits, and it is common for fruits and seeds
to be used commercially as a source of edible oils for humans, including maize, olives
and sunflower.
Complete oxidation of fats and oils produces a large amount of water. This is far more
than when the same mass of carbohydrate is respired. Desert animals like the camel and
the desert rat retain much of this ‘metabolic water’ within the body, helping them survive
when there is no liquid water for drinking. The development of the embryos of birds and
reptiles while in their shells also benefits from metabolic water formed by the oxidation
of the stored fat in their egg’s yolk. Whales are mammals surrounded by salt water they
cannot safely drink and they rely solely on metabolic water.
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Fat as a buoyancy aid
2
Fat is stored in animals as adipose tissue (Figure 2.17), typically under
the skin, where it is known as subcutaneous fat. Aquatic, diving
mammals have so much it is identified as blubber. This gives buoyancy
to the body, because fat is not as dense as muscle or bone. If fat reserves
like these have a restricted blood supply and the heat of the body is
not especially distributed to the fat under the skin (as is commonly the
case), then the subcutaneous fat also functions as a heat insulation layer.
Waterproofing of hair and feathers

Oily secretions of the sebaceous glands, found in the skin of mammals,

▲ Figure 2.17 Adipose tissue acts as a water repellent, preventing fur and hair from becoming
waterlogged when wet. Birds have a preen gland that serves the same
purpose for feathers.
Electrical insulation
Myelin lipid in the membranes of Schwann cells, forming the sheath around the axons
of neurones (page 320), electrically isolates the cell surface membrane and facilitates the
conduction of the nerve impulse there.
Phospholipids
A phospholipid has a very similar chemical structure to a triglyceride, except that one
of the fatty acids is replaced by a phosphate group. The phosphate group is ionised
and therefore water soluble. Consequently, phospholipids combine the hydrophobic
properties of the hydrocarbon tails with the water-loving (hydrophilic) properties of the
Question phosphate group.
6 Describe the A thin layer of phospholipid floats on water, forming a monolayer with the polar
properties given hydrophilic heads in water and the non-polar hydrophobic tails projecting. With more
to a lipid when it phospholipid present, the phospholipid molecules form a bilayer, with the hydrophobic
combines with a
tails aligned together. We return to this when looking into the structure of cell surface
phosphate group.
membranes (Topic 4).
phosphate group ionised

under conditions in cells
H2C COO non-polar hydrocarbon
tails of two fatty acids
condensed with glycerol
HC COO
O–
OO P O C H2
O
phosphate group has condensed

with the third —OH group of
glycerol
fatty acids
glycerol
phosphate
▲ Figure 2.18 Phospholipids
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2.3 Proteins
Learning outcomes 2
2.3.1 describe and draw the general structure of an amino acid and the
formation and breakage of a peptide bond
2.3.2 explain the meaning of the terms primary structure, secondary structure,
tertiary structure and quaternary structure of proteins
2.3.3 describe the types of interaction that hold protein molecules in shape:
2.3 Proteins
hydrophobic interactions, hydrogen bonding, ionic bonding, and covalent
bonding, including disulfide bonds
2.3.4 state that globular proteins are generally soluble and have physiological
roles and fibrous proteins are generally insoluble and have structural roles
2.3.5 describe the structure of a molecule of haemoglobin as an example of
a globular protein, including the formation of its quaternary structure
from two alpha (α) chains (α–globin), two beta (β) chains (β–globin) and
a haem group
2.3.6 relate the structure of haemoglobin to its function, including the
importance of iron in the haem group
2.3.7 describe the structure of a molecule of collagen as an example of a fibrous
protein, and the arrangement of collagen molecules to form collagen fibres
2.3.8 relate the structures of collagen molecules and collagen fibres to their
function
Starting points
★ An understanding of protein structure and how it is related to function is central
to many aspects of biology, such as enzymes, antibodies and muscle contraction.
★ Globular and fibrous proteins play important roles in biological processes such
as the transport of gases and providing support for tissues.
Proteins make up about two-thirds of the total dry mass of a cell. They differ from
carbohydrates and lipids in that they contain the element nitrogen, and usually the
element sulfur, as well as carbon, hydrogen and oxygen.
Proteins are large molecules formed from many amino acids combined in a long
chain. Typically several hundreds or even thousands of amino acid molecules are
combined together to make a protein. (So a protein can also be described as a
macromolecule.) Once the chain is constructed, a protein takes up a specific shape.
The shape of a protein is closely related to the functions it performs. We will return to
this aspect of protein structure, after we have examined the properties of individual
amino acids.
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Amino acids
2 Amino acids, as their name implies, contain two functional groups, a basic amino group
(–NH 2) and an acidic carboxyl group (–COOH). In the naturally-occurring amino acids
both functional groups are attached to the same carbon atom. Since the carboxyl group
is acidic:
Question
–COOH ∆ –COO 2 1 H1
7 What does the
symbol ‘R’ represent and the amino group is basic:
in a generalised –NH2 1 H1 ∆ –NH3
formula of an organic
an amino acid is both an acid and a base, a condition known as amphoteric.
compound?
The remainder of the molecule, the side chain or R-group, is very variable.
The bringing of amino acids together in different combinations produces proteins with
very different properties. This helps explain how the proteins in organisms are able to
fulfil the very different biological functions they have.
carbon atom to which

the two functional
groups are attached
R O
H2N C C carboxyl group

(acidic)
amino group OH
H
(basic)
the R-groups of H3C CH3

three amino acids
CH
H O CH3 O CH2 O
H2N C C H2N C C H 2N C C
H OH H OH H OH
glycine alanine leucine
▲ Figure 2.19 The structure of amino acids
The peptide bond

Two amino acids can react together with the loss of water to form a dipeptide. The
amino group of one amino acid reacts with the carboxyl group of the other, forming a
peptide bond (see Figure 2.20). Long strings of amino acids linked by peptide bonds
are called polypeptides. A peptide or protein chain is assembled, one amino acid at a
time, as we shall see later.
The terms ‘polypeptide’ and ‘protein’ can be used interchangeably but, when a
polypeptide is about 50 amino acid molecules long, it is generally agreed to be have
become a protein.
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The structure of proteins
The primary structure of a protein is the long chain of amino acids in its molecule.
Proteins differ in the variety, number and order of these amino acids. In the living 2
cell, the sequence of amino acids in the polypeptide chain is controlled by the
coded instructions stored in the DNA of the chromosomes in the nucleus (Topic 6).
Just changing one amino acid in the sequence of a protein may alter its properties
completely. This sort of ‘mistake’ or mutation does happen (see page 369).
amino acids combine together, the amino group of one with the carboxyl group of the other
2.3 Proteins
carboxyl amino
group group
R H condensation R O H H
H O H O H O
reaction
N C C + N C C N C C N C C + H2O
H OH H OH hydrolysis H OH
H R reaction H R
peptide
bond
amino acid 1 amino acid 2 dipeptide water
for example, glycine and alanine can react like this:
H H H O H H
H O H O H O
N C C + N C C N C C N C C + H2O
H OH H OH H OH
H CH3 H CH3
peptide
bond
glycine alanine glycyl-alanine
but if the amino group of glycine reacts with the carboxyl group of
alanine, a different polypeptide, alanyl-glycine, is formed
SH
H H O CH 2
three amino acids
combine together CH N C CH
to form a tripeptide C N
H2N CH COOH
O CH3 H
glycine alanine cysteine

residue residue residue
▲ Figure 2.20 Peptide bond formation
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Questions 8 The possible number of different polypeptides (P) that can be assembled is given by:
2 P = An
where A = the number of different types of amino acids available and
n = the number of amino acid monomers that make up the polypeptide molecule.
Given the naturally occurring pool of 20 different types of amino acids, calculate
how many different polypeptides are possible if constructed from 5, 25 and 50
amino acid residues respectively?
9 Distinguish between condensation and hydrolysis reactions. Give an example of
each.
The secondary structure of a protein develops when parts of the polypeptide chain take
up a particular shape, immediately after formation at the ribosome (Figure 2.21). Parts
of the chain become folded or twisted, or both, in various ways. Two major structural
forms are particularly stable and common. Either part or all of the peptide chain
becomes coiled to produce an a-helix or it becomes folded into b-sheets. These shapes
are permanent, held in place by hydrogen bonds.
The tertiary structure of a protein is the precise, compact structure, unique to that
protein that arises when the molecule is further folded and held in a particular complex
shape. This shape is made permanent by four different interactions between adjacent
parts of the chain (Figure 2.22).
The primary, secondary and tertiary structure of the protein lysozyme is shown in
Question Figure 2.23.
10 Describe three of the The quaternary structure of a protein arises when two or more polypeptides become
types of bond that held together, forming a complex, biologically active molecule. An example is haemoglobin,
maintain the tertiary found in red blood cells. This molecule consists of four polypeptide chains held around a
structure of proteins non-protein haem group, in which an atom of iron occurs (see page 52).
`-helix (rod-like) a-sheets
position of amino acid O H polypeptide chain

R H O R
residues and peptide linkages
C CH N C CH N
N C CH N C
position of amino H O R H O
peptide chain acid residues and hydrogen bond
peptide linkages in
R two β-sheets O H R O H
H
C R
C C N CH C N C
N
C N CH C N CH C
O C
H R O H R O
N
O
amino acid residue peptide chain
H hydrogen bond
C H
C
C
O C
C
R H hydrogen
O bond
▲ Figure 2.21 The secondary structure of proteins
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hydrophobic interactions
2
Hydrogen bonds are weak, but are polypeptide chain
and van der Waals forces
common in many polypeptide chains: made up of
amino acid these come into play when two or more
they help to stabilise the protein CH atoms are very close (0.3–0.4 nm apart)
residues
molecule. H3C CH3
CH2
H3C CH3 disulfide bond
O CH strong covalent bond formed
hydrogen bond H by the oxidation of —SH groups
in a hydrogen bond a hydrogen atom of two cysteine side-chains
is shared by two other atoms, e.g.
O
ionic bond
O H O C OH weak electrostatic interaction
2.3 Proteins
CH2 S S CH2 between oppositely charged
CH2 ions: may often be broken by
O H N changing the pH
N H O
O
N H N CH2 CH2 CH2 CH2 NH3+ –

O C CH2
electropositive electronegative
hydrogen atom
▲ Figure 2.22 Interactions within a polypeptide
Globular and fibrous proteins

Some proteins take up a spherical tertiary structure. They are called globular proteins.
They are generally soluble and have physiological roles in the body. Enzymes are
typically globular proteins, including lysozyme – an antibacterial enzyme present in
animal excretions such as tears (see Figure 2.23).
primary structure secondary structure

(the sequence of amino acids) (the shape taken up by parts of the amino acid chain)
Gly Arg
ValPhe Cys
H
Lys C
+H N Glu
3 C N
Leu O C O H
H O H O H O H
Ala H C
ArgLysMetAla Ala C N C CN C CN C CN C CN
His
Gly N C O C N CC N CC N CC N CC
Leu C O H O H O H O H O
Asp C H C H
Asn Tyr Ser Leu Gly O
N
C N O C H O C H O C H O C H
Gly Asn
Tyr Arg Trp O C C N CN C N CN C N CN C N CN
Phe Lys AlaAla CysVal
H H C C H O C H O C H O C H O C
Glu C N
Ser N C O
Asn
ArgAsnThr C O H
Phe Asn Asp C H C
β-sheets
Thr
AsnThrGln Ala Gly N
N
O C
Ser O C
Thr H H
Tyr Asp C
Leu Ile Gly C N
Gln N C O
AsnAsp
Ile Cys Gly
Trp O
Asn Trp Arg
SerArg Thr
Leu Ala
Ser
Pro
Gly
α-helix
Leu Cys Ser
Ser Pro Arg
Ser Ile Asn
Asn
Asp CysLeu
Ile Thr AlaSer Val
Asn
Cys
Val Ile Lys Lys Ala
Ser Val
Trp Ala
Asp Ala
Asn Trp
Gly GlyMet Arg
Asp
Asn
ValAsp Thr GlyLys CysArg
Gln
O
Ala
Trp Arg Leu C
tertiary structure
Ile ArgGlyCys
O– (the three-dimensional structure
of the protein)
▲ Figure 2.23 Lysozyme: primary, secondary and tertiary structure
Other proteins take up a tertiary structure which is a long strand, and are called fibrous
proteins. They are generally insoluble and have structural roles in the body. Examples
of fibrous proteins are fibrin, a blood protein involved in the clotting mechanism, and
keratin, found in hair, horn and nails.
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Haemoglobin
2 Haemoglobin is a globular protein (globin) consisting of four polypeptide chains (two

a-chains and two b-chains). Each polypeptide chain is associated with a non-protein
haem group, in which an iron ion (Fe²1) occurs (Figure 2.24). Since the pigment ‘haem’
is an integral part of the quaternary protein and yet is not itself made of amino acids, it
is referred to as a prosthetic group. A molecule of oxygen (O2) combines reversibly with
each haem group in the ‘pocket’ where the iron ion occurs. This reaction is dependent
upon the partial pressure of oxygen (high in the lungs, low in the respiring tissues of
the body).
haemoglobin (Hb) 1 4O2 ∆ oxyhaemoglobin (HbO8)
Within the haemoglobin molecule, the forces holding it together (and thereby
maintaining the all important three-dimensional shape of haemoglobin) are inwardly-
facing hydrophobic R-groups. On the exterior of the molecule it is the presence of
hydrophilic R-groups that maintain the solubility of the protein. Vast numbers of the
resulting more or less spherical haemoglobin molecules are normally located in the red
blood cells.
An important exception to this arises in sickle-cell anaemia, a genetically controlled
condition in which one of the amino acids that comprise the b-chain is replaced
(non-polar valine is substituted for polar glutamic acid). The result is long fibrous
haemoglobin molecules that distort and damage the red blood cells, which hinders their
efficient delivery of oxygen to the tissues. However, the sickle cell condition may confer
some resistance to malaria.
Each red blood cell contains about

280 million molecules of haemoglobin.
haem group
Each subunit is a conjugated

protein, consisting of a In haemoglobin four
protein chain (globin) attached subunits interlock to form
to a prosthetic group (haem). a compact molecule.
A prosthetic group is a
‘helper’ molecule, enabling
other molecules to be
biologically active.
globin
OH
(protein) CO
Haem is a flat molecule of
four pyrrole groups, held
together by =C– groups: at
the centre is an atom of iron(II).
CH CH2 CH3
C C
C CH C
CH3 C C CH CH2
C N N C
CH Fe 2+ CH
C N O2 N C
each iron atom of CH3 C C CH3
C CH C N
haemoglobin may porphyrin ring H2
combine loosely and C C
reversibly with a CH2 CH2
molecule of oxygen
CH2 CH2 Globin consists of 150 amino acid residues in
the form of a helix that is folded 5–7 times.
COOH COOH
▲ Figure 2.24 Haemoglobin: the quaternary protein of red cells
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Collagen
photomicrograph of collagen
fibre (× 500) – many triple
Collagen is the most abundant structural protein in animals in general. In our skin it
forms a mat in the deepest layers. It occurs in tendons, cartilage, bone, teeth and in the 2
helices bound together walls of blood vessels. It also forms the cornea of the eye.
Chemically, a collagen molecule consists of three polypeptide chains, each in the
shape of a helix. Each chain consists of about 1000 amino acids. They are wound
together as a triple helix forming a stiff cable – a unique arrangement in proteins. These
helices are stretched out, meaning this structure is not as tightly wound as an a-helix.
This structure is only able to form if every third residue in each polypeptide chain is
2.3 Proteins
glycine – the smallest amino acid. In fact, along the helix a typical repeating sequence is
glycine-proline-hydroxyproline.
The three helices are held together by numerous hydrogen bonds and have great
mechanical strength. Many of these triple helices lie side-by-side, forming collagen
fibres. Within the fibres, collagen molecules are held together by covalent cross-linkages
between the carboxyl group of one amino acid and the amino group of another. Also,
the chemical basis of the the ends of individual collagen molecules are staggered so there are no weak points in
strength of collagen collagen fibres, giving the whole structure incredible tensile strength. For example, a
three long load of at least 10 kg is needed to break a collagen fibre that is only 1 mm in diameter.
polypeptide
molecules, coiled
This quality is essential in tendons, for example. Within the body, collagen also binds
together to form strongly to other substances, such as the calcium phosphate of bone. The structure of
a triple helix
collagen is illustrated in Figure 2.25.
every third amino
acid is glycine (the
smallest amino
acid) and the other
Denaturation of protein
two amino acids Denaturation is the loss of the three-dimensional structure of a protein. It happens
are mostly proline
and hydroxyproline when the bonds that maintain the three-dimensional shape of the protein molecules are
covalent bonds
changed (Figure 2.22).
form between
the polypeptide We have noted that many of the properties and uses of proteins within cells and
chains – together organisms depend on their particular shape. When the shape of a protein changes the
with many hydrogen
bonds
protein may cease to be useful. The biochemistry of cells and organisms is extremely
sensitive to conditions that alter proteins in this way.
▲ Figure 2.25 Collagen:
an example of a fibrous Exposure to heat (or radiation) causes atoms to vibrate violently, and this disrupts
protein hydrogen and ionic bonds. Under these conditions, protein molecules become elongated,
disorganised strands. We see this when a hen’s egg is cooked. The translucent egg
‘white’ is a globular protein, albumen, which becomes irreversibly opaque and insoluble.
Exposure to heavy metal ions, to organic solvents or to extremes of acidity or alkalinity
will all trigger irreversible denaturations. These conditions sometime alter charges on
the R-groups, too.
Small changes in the pH of the medium may alter the ionic charges of acidic and basic
groups and temporarily cause change (see page 71). However, the tertiary structure may
spontaneously reform. This suggests that it is the primary structure of a protein that
determines cross-linking and the tertiary structure, given a favourable medium.
The making of macromolecules – a review

We began this topic by introducing four elements – carbon, hydrogen, oxygen and
nitrogen. We saw that it is from atoms of these elements that the carbohydrates, lipids
and proteins are made – the bulk of the molecules of life. These biological molecules
exist in a huge range of sizes, all of them with important roles in working cells.
However, some of the molecules in cells are very large indeed. These are the giant
molecules, known as macromolecules. Polysaccharides and proteins are the
macromolecules that have been introduced in this topic. Chemically we have described
them as polymers, made by linking together similar building blocks called monomers.
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Proteins are built from amino acids and polysaccharides from monosaccharide
Question
sugars.
2 11 Explain why
polysaccharides Monomers are linked together by a reaction in which the elements of water are
and proteins removed (a condensation reaction). So the monomer units that have made up a
are described as polymer are now called residues. The reverse reaction requires water and it results
macromolecules but in the release of individual monomers again. It is called a hydrolysis reaction. The
lipids are not. bonds between monomers are covalent bonds. Between monosaccharide residues of a
polysaccharide they are glycosidic bonds. Between amino acid residues of a protein,
peptide bonds are formed.
The other macromolecules found in cells are the nucleic acids. These are discussed in
Topic 6.
The most significant points to keep in mind about the properties of macromolecules are:
» the type of macromolecule depends upon the type of monomer from which it is built
» the order in which the monomers are combined decides the shape of the
macromolecule
» the shape of the macromolecule decides its biological properties and determines its
role in cells.
As the functions of each of the macromolecules of cells – polysaccharides, proteins
and (later) nucleic acids are discussed, the significance of ‘type’, ‘order’ and ‘shape’ will
become clear.
Roles of proteins
We have seen that some proteins of organisms have a structural role in cells and
organisms; others have biochemical or physiological roles. Whatever their roles
are in metabolism, however, cell proteins are in a continuous state of flux. They are
continuously built up, used and broken down again into their constituent amino acids,
to be rebuilt or replaced by fresh proteins, according to the needs of the cells
(Figure 2.26).
Types and roles

in animals amino acids nucleus controls and directs
obtained by digestion and protein synthesis via mRNA
absorption (heterotrophic nutrition) structural proteins
(fibrous proteins), e.g. keratin of hair
collagen of skin and bone,
(Figure 2.25)
enzymes (biological catalysts)
synthesis of organelles and cytosol (Topic 3)
continual breakdown and
rebuilding of proteins means muscles/movement proteins e.g.
amino acid the nucleus is able to myosin and actin of muscle myofibrils
‘pool’ in frequently update its proteins (Figure 12.12, page 255)
cytoplasm command of cell metabolism
transport proteins e.g.
and cell structure haemoglobin of red blood cells
breakdown (Figure 2.24)
defence against disease proteins –
antibodies (immunoglobulins)
secreted by B-lymphocytes
(Topic 11)
in plants amino acids obtained
by synthesis from NH2 and organic protein of membranes – part
acids (autotrophic nutrition) structural, also as enzymes,
pumps and receptors
(Topic 4)
▲ Figure 2.26 The dynamic state of cell proteins
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2.4 Water
Learning outcomes 2
2.4.1 explain how hydrogen bonding occurs between water molecules and
relate the properties of water to its roles in living organisms, limited to
solvent action, high specific heat capacity and latent heat of vaporisation
2.4 Water
Starting point
★ Water is a special molecule with extraordinary properties that make life possible
on this planet 150 million kilometres from the Sun.
Living things are typically solid, substantial objects, yet water forms the bulk of their
structures. Between 65 and 95 per cent by mass of most multicellular plants and animals
(about 80 per cent of a human cell) consists of water. Despite this, water is a substance
that is often taken for granted.
Water is composed of atoms of the elements hydrogen and oxygen. One atom of
oxygen and two atoms of hydrogen combine by sharing of electrons (covalent
bonding). However, the water molecule is triangular rather than linear and the
nucleus of the oxygen atom draws electrons (which are negatively charged) away from
the hydrogen nuclei (which are positively charged) – with an interesting consequence
(Figure 2.27, overleaf). Although overall the water molecule is electrically neutral,
there is a net negative charge on the oxygen atom (conventionally represented by
Question Greek letter delta as  2) and a net positive charge on the hydrogen atoms (represented
by 1). In other words, the water molecule carries an unequal distribution of
electrical charge within it. This unequal distribution of charge is called a dipole.
ionic and covalent
Molecules which contain groups with dipoles are known as polar molecules. Water
bonding.
is a polar molecule.
Hydrogen bonds
With water molecules, the positively charged hydrogen atoms of one molecule are
attracted to the negatively charged oxygen atoms of nearby water molecules by forces
called hydrogen bonds. These are weak bonds compared to covalent bonds, yet they are
strong enough to hold water molecules together. Hydrogen bonds largely account for the
unique properties of water. We examine these properties next.
Meanwhile we can note that dipoles are found in many different molecules,
especially where there occurs an –OH, –C5O or >N–H group. Hydrogen bonds can
form between all these groups and also between these groups and water. Materials
with an affinity for water are described as hydrophilic (meaning ‘water-loving’, see
next page).
The properties of water

Heat energy and the temperature of water
A lot of heat energy is required to raise the temperature of water. This is because much
energy is needed to break the hydrogen bonds that restrict the movements of water
molecules. This property of water is its specific heat capacity. The specific heat capacity
of water is the highest of any known substance. Consequently, aquatic environments
like streams, rivers, ponds, lakes and seas are very slow to change temperature when
the surrounding air temperature changes. Aquatic environments have much more stable
temperatures than do terrestrial (land) environments.
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one oxygen atom combines unshared electrons
with two hydrogen atoms by (negative charge)
2 sharing electrons (covalent

bond)
nucleus of
oxygen atom
shared electrons
in the water molecule the
oxygen nucleus draws
electrons (negatively nucleus of hydrogen
charged) away from the atom (proton –
hydrogen nucleus (positively positive charge)
charged)
angle about
the water molecule carries 105º
an unequal distribution of
electrical charge, even
though overall it is Note the water molecule is
electrically neutral triangular in shape, not linear.
small
negative –
charge
polar water molecule
there is electrostatic small

attraction between the positive +
positively charged region of charge
one water molecule and the
negatively charged region of
a neighbouring one, giving hydrogen bond hydrogen bond
rise to weak bonds called
hydrogen bonds
▲ Figure 2.27 The water molecule and the hydrogen bonds it forms
Another consequence is that cells and the bodies of organisms do not change
temperature readily. Bulky organisms, particularly, tend to have a stable temperature in
the face of rising or falling external temperatures.
Evaporation and heat loss

The hydrogen bonds between water molecules make it difficult for them to be separated
and vapourised (i.e. evaporated). This means that much energy is needed to turn liquid
water into water vapour (gas). This amount of energy is the latent heat of vaporisation and
for water it is very high. Consequently, the evaporation of water in sweat on the skin or in
transpiration from green leaves causes marked cooling. The escaping molecules take a lot
of energy with them. You experience this when you stand in a draught after a shower. And,
since a great deal of heat is lost with the evaporation of a small amount of water, cooling by
evaporation of water is economical on water too.
The solvent properties of water

Water is a powerful solvent for polar substances. These include:
» ionic substances such as sodium chloride (Na1 and Cl 2). All cations (positively
charged ions) and anions (negatively charged ions) become surrounded by a shell of
orientated water molecules (Figure 2.28)
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Ionic compounds like
NaCl dissolve in water,
NaCl Na++ Cl– 2

with a group of orientated
water molecules
around each ion:
Cl– Na+
2.4 Water
Sugars and alcohols
dissolve due to hydrogen
bonding between polar CH2OH
groups in their molecules
(e.g. — OH) and the polar H C O H
water molecules: H
C OH H C
OH C C OH
H OH
▲ Figure 2.28 Water as universal solvent
» carbon-containing molecules with ionised groups (such as the carboxyl group –

COO 2 or the amino group –NH31). Soluble organic molecules like sugars dissolve in
water due to the formation of hydrogen bonds with their slightly charged hydroxyl
groups (–OH), for example.
Once they have dissolved, molecules (the solute) are free to move around in the water
Question
(the solvent) and, as a result, are more chemically reactive than when in the undissolved
13 Water has a relative solid.
molecular mass
of only 18 yet it is We have noted that molecules with an affinity for water are described as hydrophilic.
a liquid at room On the other hand, non-polar substances are repelled by water, as in the case of oil on
temperature. This the surface of water. Non-polar substances do not contain dipoles and are hydrophobic
contrasts with other (water-hating).
small molecules
which are gases. (For Property Benefit to life
example, methane 1 A liquid at room temperature, Liquid medium for living things and for the
(CH4) with a relative water dissolves more substances chemistry of life.
molecular mass of than any other common liquid.
16; ammonia (NH3)
2 Much heat energy is needed to Aquatic environments are slow to change
with a relative
raise the temperature of water. temperature.
molecular mass of 17
and carbon dioxide Bulky organisms have stable temperatures.
(CO2) with a relative 3 Evaporation requires a great deal Evaporation causes marked cooling. Much heat
molecular mass of of heat. is lost by the evaporation of a small quantity
44.) What property of water.
of water molecules
4 Water molecules adhere to Water adheres to the walls of xylem vessels as
may account for this?
surfaces. Water column does not it is drawn up the stem to the leaves from the
break or pull apart under tension roots. Water can be lifted by forces applied
(see Topic 7). at the top, and so can be drawn up the xylem
vessels of a tree trunk by forces generated in
the leaves.
▲ Table 2.2 Water and life – a summary
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SUMMARY
2 » Tests can be carried out to identify reducing sugars, ester bonds. The fatty acids may be saturated or
non-reducing sugars, starch and proteins. The unsaturated (containing one or more double bonds
Benedict’s test can be modified to estimate the between carbon atoms in the hydrocarbon tails).
concentration of reducing sugar. Fats and oils are effectively energy stores.
» Organic compounds contain the elements carbon » In phospholipids, one of the hydroxyl groups
and hydrogen, usually with oxygen and other of glycerol reacts with a phosphate group. The
elements. Carbon atoms form strong, covalent product has a hydrocarbon ‘tail’ (hydrophobic) and
bonds (sharing electrons between atoms) with an ionised phosphate group (hydrophilic) so they
other carbon atoms and with atoms of other form bilayers on water and form the membranes of
elements, forming a huge range of compounds. cells (along with proteins).
Many of the organic compounds of life fall into one » Proteins contain nitrogen and (often) sulfur, in
of the four groups of compounds: carbohydrates, addition to carbon, hydrogen and oxygen. The
lipids, proteins or nucleic acids. building blocks of proteins are amino acids, and
» Carbohydrates contain carbon, hydrogen many hundreds or thousands of amino acid
and oxygen only, and have the general residues form a typical protein. Amino acids have
formula of Cx(H2O)y. They consist of the a basic amino group (–NH2) and an acidic carboxyl
sugars (monosaccharides and disaccharides) group (–COOH) attached to a carbon atom to which
and macromolecules built from sugars the rest of the molecule (–R) is also attached.
(polysaccharides). » Of the many amino acids that occur, only 20 are
» Monosaccharides include the six-carbon sugars built up to make the proteins of living things. Amino
(hexoses), such as glucose and fructose. They are acids combine by peptide bonds between the
important energy sources for cells. The hexoses carboxyl group of one molecule and the amino
have the same molecular formula (C6H12O6) group of the other to form a polypeptide chain.
but different structural formulae. Two hexose Proteins, too, are polymers.
monosaccharides combine together with the » The properties of polypeptides and proteins are
removal of water (a condensation reaction) to form determined by the amino acids they are built
a disaccharide sugar, held together by a glycosidic from and the sequence in which the amino acids
bond. For example, the disaccharide sucrose is occur. The sequence of amino acids is the primary
formed from glucose and fructose. structure of the protein and is indirectly controlled
» Monosaccharides (and some disaccharides) by the nucleus.
are reducing sugars. When heated with alkaline » The shape the protein molecule takes up also
copper(II) sulfate (Benedict’s solution), which is determines its properties. Part of a polypeptide
blue, they produce reduced copper(I) oxide, which chain may form into a helix and part into sheets
is a brick red precipitate. The sugar is oxidised to a (the secondary structure of a protein). The whole
sugar acid. Sucrose is not a reducing sugar. chain is held in position by bonds between parts
» Most polysaccharides are built from glucose folded together, forming the tertiary structure
units condensed together. They are examples of a protein. Separate polypeptide chains may
of polymers consisting of a huge number of combine, sometimes with other substances, to
monomers, such as glucose, condensed together. form the quaternary structure.
They may be food stores (e.g. starch, glycogen) or » Fibrous proteins have a structural role in the body,
structural components of organisms (e.g. cellulose, for example, collagen of skin, bone and tendon.
chitin). They are generally insoluble. Globular proteins are
» Lipids contain the elements carbon, hydrogen and generally soluble and have a physiological role in
oxygen but the proportion of oxygen is low. They the body, for example many enzymes, antibodies
are hydrophobic, non-polar and insoluble in water and hormones.
but otherwise form a diverse group of compounds, » Water is electrically neutral but, because of
including the fats and oils. These latter compounds its shape, it carries an unequal distribution of
leave a cloudy white suspension in the emulsion charge – it is a polar molecule (oxygen with a small
test . negative charge, hydrogen with a small positive
» Fats are solids at room temperature; oils are charge). Consequently, water forms hydrogen
liquids. They are formed by a condensation reaction bonds with other water molecules. These hydrogen
between the hydroxyl groups of glycerol and bonds are responsible for the properties of water
three fatty acids, forming a triglyceride, with important to life.
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1 a Sucrose is a disaccharide. Fig. 1.1 shows how sucrose is broken down in a 2
reaction with hydrochloric acid.
CH2OH
H O H HOCH2 O H
H
OH H O H HO
HO CH2OH
H OH OH H

+H2O
CH2OH
H O H HOCH2 O H
H
OH H H HO
HO OH HO CH2OH
H OH OH H
A B
▲ Fig. 1.1
i Name the products, A and B, of the reaction shown in Fig. 1.1. [2]
ii Name the type of bond that is broken in the reaction shown in Fig. 1.1. [1]
iii State the type of reaction shown in Fig. 1.1. [1]
b When Benedict’s solution is added to a sucrose solution and put into a boiling
water-bath, no change in colour is observed. State why no colour change is
observed. [2]
[Total: 6]
(Cambridge International AS and A Level Biology 9700 Paper 21 Q2 a, b May/June 2018)
2 a Cellulose and collagen are macromolecules. What do you understand by
the term ‘macromolecule’? [2]
b When cellulose and collagen are hydrolysed by appropriate enzymes,
what are the products in each case? [2]
c By means of fully annotated skeletal formulae of parts of adjacent
cellulose molecules, explain how cellulose is formed from its component
monosaccharide. Explain how this molecular structure is the basis of the
distinctive property of cellulose. [6]
d Describe the steps to the test you would need to show whether the
monosaccharide formed by hydrolysis was a reducing sugar.
What result would you expect? [3]
e Where does collagen occur in the human body? [1]
f By means of fully annotated skeletal formulae of parts of adjacent
collagen molecules, explain how collagen is formed from its component
monomers, and the basis of the distinctive property of collagen. [6]
[Total: 20]
3 a The angle between the oxygen–hydrogen bonds in water is about 1508. By
means of a fully annotated diagram only, explain why the existence of this
angle causes the water molecule to be polar (although overall it is electrically
neutral).
b Outline four of the unusual properties of water that can be ascribed to the
effect of hydrogen bonds and summarise the significance of each for living
things.
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4 a Chemists often represent the structure of organic molecules as skeletal
formulae in which the C and H atoms are left out. Write the skeletal
2 formulae for two molecules of amino acid and show the reaction and
products of a condensation reaction between them. On your diagram,
identify and name the bond that is formed between the two molecules. [4]
b To two test tubes, one with 2 cm3 of a dilute egg white solution and one with
2 cm3 of a dilute starch solution, was added 2 cm3 of a dilute sodium hydroxide
solution and the contents gently shaken. Then a dilute copper(II) sulfate
solution was added to each, drop by drop. The tubes were gently shaken
between additions, and this procedure was continued until a definite colour
could be seen. What colours would have appeared in the two tubes, and
what do the results indicate? [4]
c Explain concisely what is meant by the following structures of a protein,
such as haemoglobin.
i Primary [2]
ii Secondary [2]
iii Tertiary [2]
iv Quaternary [2]
d In addition to hydrogen bonds, three other types of bond are important in the
secondary and tertiary structure of a protein. Name and explain the chemical
nature of these additional bonds. [6]
[Total: 22]
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AS LEVEL
3 Enzymes
3.1 Mode of action of enzymes

Enzymes are essential for life Learning outcomes
to exist. The mode of action
of enzymes and the factors By the end of this topic, you will be able to:
that affect their activity are 3.1.1 state that enzymes are globular proteins that catalyse reactions inside
explored in this topic. Prior cells (intracellular enzymes) or are secreted to catalyse reactions outside
knowledge for this topic cells (extracellular enzymes)
is an understanding that 3.1.2 explain the mode of action of enzymes in terms of an active site, enzyme–
an enzyme is a biological substrate complex, lowering of activation energy and enzyme specificity,
catalyst that increases
including the lock-and-key hypothesis and the induced-fit hypothesis
the rate of a reaction and
remains unchanged when the 3.1.3 investigate the progress of enzyme-catalysed reactions by measuring
reaction is complete. rates of formation of products using catalase and rates of disappearance
of substrate using amylase
There are many
opportunities in this
3.1.4 outline the use of a colorimeter for measuring the progress of enzyme-
topic for students to gain catalysed reactions that involve colour changes
experience of carrying out
practical investigations and
analysing, interpreting and Starting point
evaluating their results.
★ There are many different enzymes, each one specific to a particular reaction.
This specificity is the key to understanding the efficient functioning of cells
and living organisms.

Introducing enzymes and their role in metabolism
Enzymes are globular proteins that catalyse the many thousands of metabolic reactions
taking place within cells and organisms. Metabolism is the name we give to these
chemical reactions of life. The molecules involved are collectively called metabolites.
Many of these metabolites are made in organisms. Other metabolites have been
imported from the environment, such as from food substances taken in, water and the
gases carbon dioxide and oxygen.
Metabolism actually consists of chains (linear sequences) and cycles of enzyme-
catalysed reactions, such as we see in respiration (page 248), photosynthesis (page 275),
protein synthesis (page 131) and very many other pathways. These reactions may be
classified as one of just two types, according to whether they involve the build-up or
breakdown of organic molecules.
» In anabolic reactions, larger molecules are built up from smaller molecules.
Examples of anabolism are the synthesis of proteins from amino acids and the
synthesis of polysaccharides from simple sugars.
» In catabolic reactions, larger molecules are broken down. Examples of catabolism
are the digestion of complex foods and the breakdown of sugar in respiration.
Enzymes as globular proteins

In Topic 2 we saw that the tertiary structure of globular proteins was typically spherical.
In these molecules their linear chain of amino acids (primary structure) is precisely folded
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synthesis of complex and held in a globular three-dimensional shape containing α-helices and β-sheets. Also,
molecules used in growth
the R-groups of the amino acids present on the exterior of the molecule are hydrophilic
3
and development and in
metabolic processes, groups, making the protein water soluble. Remember, this structure contrasted with that
e.g. proteins,
polysaccharides,
of the fibrous proteins, such as collagen.
lipids, hormones, growth
factors, haemoglobin,
chlorophyll
Enzymes as biological catalysts
A catalyst is a molecule that speeds up a chemical reaction but remains unchanged at the end
anabolism:
energy-requiring
of the reaction. Most chemical reactions do not occur spontaneously. In a laboratory or in an
reactions, i.e. industrial process, chemical reactions may be made to occur by applying high temperatures,
3 Enzymes
endergonic high pressures, extremes of pH and by keeping a high concentration of the reacting molecules.
reactions
If these drastic conditions were not applied, very little of the chemical product would be
sugars, formed. In contrast, in cells and organisms, many of the chemical reactions of metabolism
amino acids,
fatty acids,
occur at exactly the same moment, at extremely low concentrations, at normal temperatures
nutrients and under the very mild, almost neutral, aqueous conditions we find in cells.
i.e. smaller
organic
molecules How is this brought about?
catabolism For a reaction between two molecules to occur there must be a successful collision
energy-releasing between them. The molecules must collide with each other in the right way and at
reactions,
i.e. exergonic the right speed. If the angle of collision is not correct, the molecules bounce apart.
reactions Alternatively, if the speed of the collision speed is wrong or the impact is too gentle, for
release of simple example, then there will be insufficient energy for the rearrangement of electrons. Only
substances, if the molecules are lined up and collide with the correct energies does a reaction occur.
e.g. small inorganic
molecules, CO2, H2O, The ‘right’ conditions happen so rarely that the reaction doesn’t happen to a significant
mineral ions
extent normally. If we introduce extreme conditions, such as those listed above, we
▲ Figure 3.1 Metabolism: can cause the reaction to happen. On the other hand, if we introduce an enzyme for
an overview
this particular reaction then the reaction occurs at great speed. Enzymes are amazing
molecules in this respect.
Where do enzymes operate?

Some enzymes are exported from cells, such as the digestive enzymes. Enzymes, like
these, that are parcelled up, secreted and work externally are called extracellular
enzymes. However, very many enzymes remain within the cells and work there.
These are intracellular enzymes. They are found inside organelles, in the membranes
of organelles, in the fluid medium around the organelles (the cytosol) and in the cell
surface membrane.
Enzymes control metabolism

There is a huge array of enzymes that facilitate the chemical reactions of the metabolism.
Since these reactions can only take place in the presence of specific enzymes, we know
that if an enzyme is not present then the reaction it catalyses cannot occur.
Many enzymes are always present in cells and organisms but some enzymes are
produced only under particular conditions or at certain stages. By making some
enzymes and not others, cells can control what chemical reactions happen in the
cytoplasm. Sometimes it is the presence of the substrate molecule that triggers the
synthesis of the enzyme. In Topic 4 we see how protein synthesis (and therefore enzyme
production) is directly controlled by the cell nucleus.
How enzymes work

So, enzymes are biological catalysts made of protein. They speed up the rate of a
chemical reaction. The general properties of catalysts are:
» they are effective in small amounts
» they remain unchanged at the end of the reaction.
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The presence of enzymes enables reactions to occur at incredible speeds, in an
orderly manner, yielding products that the organism requires, when they are needed.
Sometimes reactions happen even though the reacting molecules are present in very low
concentrations.
3
How is this brought about?
CH2OH
1 The reaction: hydrolysis of sucrose
oxygen bridge from water
to form glucose and fructose O
CH2OH

1 HO
OH CH2OH O CH2OH
O O O
HO +
2
OH OH OH
HO HOH 2C HOH 2C
HO OH
H O
water H OH HO OH
sucrose glucose fructose
sucrose sucrose sucrose

2 Random collision possibilities:
when sucrose and water collide at
the wrong angle
water
water water
sucrose sucrose sucrose

when sucrose and water collide at
the wrong speed
These events are what happens at

most random collisions.
water water
water
For the reaction to occur, sucrose sucrose glucose

and water must collide in
just the right way – glucose and
fructose are formed
Under normal conditions this

water fructose
happens so very infrequently
it is an insignificant event.
3 In the presence of one molecule of the enzyme sucrase (invertase),

approximately 3.0 × 104 molecules of sucrose are hydrolysed each minute.
▲ Figure 3.2 Can a reaction occur without an enzyme?
Enzymes lower the activation energy

As molecules react they become unstable, high energy intermediates, but they are in
this state only momentarily. We say they are in a transition state because the products
are formed immediately. The products have a lower energy level than the substrate
molecules. Energy is needed to raise molecules to a transition state and the minimum
amount of energy needed to do this is called the activation energy. It is an energy
barrier that has to be overcome before the reaction can happen. Enzymes work by
lowering the amount of energy required to activate the reacting molecules.
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‘boulder on hillside’ model of activation energy without a catalyst, this
amount of energy needs
3
triggering the fall,
to be put in to start the effect of catalyst
either by pushing
reaction
or by removing
the hump (the
enzyme way)
activation energy
3 Enzymes
energy
free energy change
products
(at lower
energy level)
reactant products
▲ Figure 3.3 Activation energy
A model of what is going on is the boulder (the substrate) perched on a slope, prevented
from rolling down by a small hump (the activation energy) in front of it. The boulder can be
pushed over the hump. Alternatively, the hump can be dug away (the activation energy can
be lowered), allowing the boulder to roll and shatter at a lower level (into the products).
The enzyme has an active site

In a reaction catalysed by an enzyme, the starting substance is called the substrate. It
is converted to the product. The way an enzyme works is for the substrate molecule to
become attached (we say ‘bind to’) the enzyme at a specially formed pocket in the enzyme –
very briefly. This binding point is called the active site. The active site takes up a relatively
small part of the total volume of the enzyme.
So, an enzyme (E) works by binding to its substrate (S) molecule at a specially formed
pocket in the enzyme. This concept is referred to the lock-and-key hypothesis of
enzyme action. As the enzyme and substrate form a complex (E–S), the substrate is
raised in energy to a transition state and then breaks down into products (Pr) plus
unchanged enzyme.
The sequence of steps to an enzyme-catalysed reaction:
E 1 S → E–S → Pr 2 E
enzyme + substrate E–S complex product + enzyme available for reuse
Enzymes are typically
(substrate raised to large globular protein
transition state)
substrate molecule – molecules. Most substrate
E + S E–S Pr + E the key molecules are quite
small molecules by
comparison. Even when
active site (here the substrate molecules
the substrate
molecule is held are very large, such as
and reaction occurs) – enzyme–substrate certain macromolecules
the lock enzyme
complex like the polysaccharides,
(large protein
molecule) only one bond in the
substrate is in contact
with the active site of the
enzyme.
substrate
product molecule now at
molecules transition state
▲ Figure 3.4 The lock-and-key hypothesis of enzyme action

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Enzymes are highly specific
Enzymes are highly specific in their action. They catalyse only one type of reaction or
only a very small group of very similar reactions. 3
This means that an enzyme ‘recognises’ a very small group of substrate molecules or
even only a single type of molecule. This is because the active site where the substrate
molecule binds has a precise shape and distinctive chemical properties (meaning the
presence of particular chemical groups and bonds). Only particular substrate molecules
can fit to a particular active site. All other substrate molecules are unable to fit and so
cannot bind.
Question

1 Explain why the Catalysis by ‘induced fit’
shape of globular We have seen that enzymes are highly specific in their action. This makes them different
proteins that from most inorganic catalysts. Enzymes are specific because of the way they bind with their
are enzymes is substrate at a pocket or crevice in the protein. The lock-and-key hypothesis, however, does
important in enzyme
not fully account for the combined events of ‘binding’ and simultaneous chemical change
action?
observed in most enzyme-catalysed reactions.
polypeptide of 49 amino acid residues,

making up a simple enzyme
substrate
active site (pocket/crevice

in the protein molecule)
The amino acids in a

protein have different
roles.
The substrate molecule
combines (temporarily)
with the enzyme by
inducing a change in
shape of the enzyme
molecule.
the induced-fit process plays a
part in bringing about the chemical
changes, which are the enzyme-
catalysed reaction
some amino acid residues
match certain groupings on the
substrate molecule, enabling the
enzyme–substrate complex to form,
3 e.g. residues 3–4–5 and 24–25–26
4
5 other amino acid
residues are ‘reactive’,
substrate
i.e. catalytic residues
that induce the
41
breaking of bonds,
20 and the formation
Specificity: of product(s),
24 25 26
• Some amino acid residues allow a e.g. 20 and 41
particular substrate molecule to ‘fit’
• Some amino acid residues bring about other amino acid residues interact to form the
particular chemical changes. three-dimensional structure of the enzyme
▲ Figure 3.5 The induced fit hypothesis of enzyme action
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At the active site, the arrangement of certain amino acid molecules in the enzyme
exactly matches certain groupings on the substrate molecule, enabling the enzyme–
3 substrate complex to form. As the complex is formed, an essential, critical change of
shape is caused in the enzyme molecule. It is this change of shape that is important
in momentarily raising the substrate molecule to the transitional state. It is then able
to react.
With a transitional state achieved, other amino acid molecules of the active site bring
about the breaking of particular bonds in the substrate molecule, at the point where
it is temporarily held by the enzyme. It is because different enzymes have different
3 Enzymes
arrangements of amino acids in their active sites that each enzyme catalyses either a single
chemical reaction or a group of closely related reactions.
slight change in
shape of active
site as substrate
molecule fits,
glucose
and reaction
+ ATP takes place
Question
2 a D
efine the term
‘catalyst’. two polypeptide
chains make up
b List two the enzyme
differences
hexokinase
between inorganic (computer-generated
catalysts and molecular model)
enzymes. ▲ Figure 3.6 Computer-generated image of the induced fit hypothesis in action
Naming enzymes
Many enzymes have a name based on the name of their substrate, with the ending -ase
added. For example, lactase hydrolyses lactose and amylase hydrolyses amylose.
Other enzymes have been given names that tell us little or nothing about what they do,
such as many of the enzymes of digestion, for example, pepsin, trypsin and rennin.
Today, systematic naming of enzymes is based on an agreed classification of enzymes
and on the name of the substrate catalysed. These types of names are long and detailed.
They are outside the scope of this book. They are used in the communications of
enzymologists but not in everyday usage. However, you are already familiar with certain
enzymes. For example, the enzymes that catalyse the formation of two products from a
larger substrate molecule by a hydrolysis reaction are classified as ‘hydrolases’. Can you
name a hydrolase?
Studying enzyme-catalysed reactions

Enzyme-catalysed reactions are fast reactions. We know this from the very large
numbers of substrate molecules converted to products by a mole of enzyme in one
minute. The mole is a unit for the amount of a substance.
The enzyme catalase catalyses the breakdown of hydrogen peroxide. This enzyme is a
good example to use in studying the rate of enzyme-catalysed reactions.
catalase
2H2O2 2H2O 1 O2
Catalase occurs widely in the cells of living things. It functions as a protective
mechanism for the delicate biochemical machinery of cells. This is because hydrogen
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fresh liver small blocks
tissue of tissue cut
tissue treated with
boiling water for
3 minutes then
3
cooled
20 cm3 of
‘10 volume’ no gas
H2O2 solution evolved
violent liberation
of oxygen gas

▲ Figure 3.7 Liver tissue in dilute hydrogen peroxide solution
peroxide is a common by-product of some of the reactions of metabolism. Hydrogen

peroxide is a very toxic substance – a very powerful oxidising agent. Catalase inactivates
hydrogen peroxide as soon as it forms, before damage can occur.
You can demonstrate the presence of catalase in fresh liver tissue by dropping a small
piece into dilute hydrogen peroxide solution (Figure 3.7). Compare the result obtained
with that from a similar piece of liver that has been boiled in water (high temperature
denatures and destroys enzymes, including catalase). If you do not wish to use animal
tissues, then you can use potato or soaked and crushed dried peas instead – the results
will be equally dramatic.
Measuring the rate of reaction

In practical terms, the rate of an enzyme-catalysed reaction is taken as the amount of
substrate that has disappeared from a reaction mixture in a given time. Alternatively, the
amount of product that has accumulated in a period of time can be measured. For example,
in Figure 3.8 (next page), the enzyme amylase is used to digest starch to sugar, and here it is
the rate that the substrate starch disappears from a reaction mixture that is measured.
Working with catalase, however, it is easiest to measure the rate at which the product
(oxygen) accumulates. In the experiment illustrated in Figure 3.8, the volume of oxygen
that has accumulated at half minute intervals is recorded on the graph.
In both of these examples we find that, over a period of time, the initial rate of reaction
is not maintained but, rather, falls off quite sharply. This is typical of enzyme actions
studied outside their location in the cell. Can you think of reasons why?
The fall-off can be due to a number of reasons. Most commonly it is because the
concentration of the substrate in the reaction mixture has fallen. Consequently, it is the
initial rate of reaction that is measured. This is the slope of the tangent to the curve in
the initial stage of reaction. How this is calculated is shown in Figure 3.8.
Question 3 In an investigation of oxygen production from hydrogen peroxide solution by the

enzyme catalase the following results were obtained.
Time of readings (s) 0 20 40 60 80 100 120

Volume of O2 produced 0 43 66 78 82 91 92
(cm3)
a Plot a graph to show oxygen production against time.

b From your graph, find the initial rate of the reaction.
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delivery
tube
3
The test tube is tipped up
to mix the enzyme solution oxygen produced,
with the substrate. collected by downward
displacement of water
in an inverted measuring
cylinder
catalase
solution
hydrogen
3 Enzymes
peroxide
solution
(10 volume)
stopclock
recorded
The rate of an enzyme

reaction is greatest at the start,
the initial rate.
30
Gas volume
e
Time/s
rat
25 actual rate collected/cm3

ial
volume of oxygen
init
30 6
produced/cm3
20 60 12
results 90 16
15 plotted 120 19
150 22
10
180 23
5 210 24
240 25
from
the 270 25.5
graph 30 120 180 240 360 300 26
time/s
If the initial rate of O2 production continued for 120 s, then 28 cm3 of O2 would be produced.
28
Therefore the initial rate = cm3 s–1
120
= 0.23 cm3 s–1
▲ Figure 3.8 Measuring the rate of reaction using catalase
Using a colorimeter to measure the progress of enzyme-

catalysed reactions
In many enzyme-catalysed reactions, the appearance (or disappearance) of a coloured
compound may be observed, indicating the progress of the reaction. Such reactions can
be measured or quantified using a colorimeter, a light-sensitive instrument that measures
the transmittance or absorbance of light passing through a liquid sample (Figure 3.9).
The colorimeter measures the intensity of the colour (optical density) that develops in
such chemical reactions. The colour of the light can be changed by selecting a particular
coloured filter – the colour is chosen so that it is the frequency of light which is absorbed by
the sample.
The absorbance of a series of solutions of known concentration is first measured and a
graph of concentration against absorbance is plotted. This gives a calibration curve.
The absorbance of the unknown sample can be read from the curve to give the
concentration of the unknown solution.
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a)
3.2 Factors that affect enzyme action

b)
light of a less
white selected intense
light frequency light
light source filter tube light-sensitive

containing cell and meter
sample
▲ Figure 3.9 a) A cuvette being placed in a colorimeter; b) simplified diagram of colorimeter
For example, when using methylene blue to investigate the effect of temperature on the
rate of respiration of a suspension of yeast cells (see page 258), a colorimeter could be
used to measure the rate of decolourisation of methylene blue.

Learning outcomes
3.2.1 investigate and explain the effects of the following factors on the
rate of enzyme-catalysed reactions: temperature, pH (using buffer
solutions), enzyme concentration, substrate concentration and inhibitor
concentration
3.2.2 explain that the maximum rate of reaction (Vmax) is used to derive the
Michaelis–Menten constant (Km), which is used to compare the affinity of
different enzymes for their substrates
3.2.3 explain the effects of reversible inhibitors, both competitive and non-
competitive, on enzyme activity
3.2.4 investigate the difference in activity between an enzyme immobilised in
alginate and the same enzyme free in solution, and state the advantages
of using immobilised enzymes
Starting point
★ Investigating the effects of factors on enzyme activity gives opportunities for
planning and carrying out experiments under controlled conditions.
Investigating factors that affect the rate

of reaction of enzymes
Enzymes are sensitive to environmental conditions – very sensitive, in fact. Many factors
within cells affect enzymes and therefore alter the rate of the reaction being catalysed.
Investigations of these factors, including temperature, pH and the effect of substrate
concentration in particular, have helped our understanding of how enzymes work.
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blue–black = starch
3
the sequence of colour red = maltose
glass rod changes observed is:
yellow–brown = all carbohydrate is
present as monosaccharide
I2/KI solution
5 cm3 amylase solution

3 Enzymes
mixed
5 cm3 starch solution
water bath water
at selected
temperature
white tile
The glass rod was rinsed before
returning to the reaction
mixture to remove any traces
of I2/KI solution.
stop clock
The experiment is repeated at a range of temperatures, such as at 10, 20, 30, 40, 50 and 60°C.
A control tube of 5 cm3 of starch solution + 5 cm3 of distilled water (in place of the enzyme) should
be included and tested for the presence/absence of starch, at each temperature used.
▲ Figure 3.10 The effect of temperature on hydrolysis of starch by amylase
Other variables – such as the concentrations of the enzyme and substrate Temperature
solutions – were kept constant.
Examine the investigation of the effect of
Up to about 40ºC the rate increases – a 10ºC rise temperature on the hydrolysis of starch by the
in temperature is accompanied by an approximate
enzyme amylase shown in Figure 3.10. When
doubling of the rate of reaction.
starch is hydrolysed by the enzyme amylase, the
high product is maltose, a disaccharide. Starch gives
time, e.g. per second) in arbitrary units
rate
a blue–black colour when mixed with iodine
amount of product formed per unit
rate of enzyme-catalysed reaction
(amount of substrate used up or
solution (iodine in potassium iodide solution)

but maltose gives a red colour. The first step
Now the enzyme- in this experiment is to bring samples of the
catalysed reaction enzyme and the substrate (the starch solution) to
rate decreases,
owing to the
the temperature of the water bath before being
denaturation of mixed – a step called ‘pre-incubation’.
the enzyme and
destruction of The progress of the hydrolysis reaction is then
active sites. followed by taking samples of a drop of the
mixture on the end of the glass rod, at half
low minute intervals. These are tested with iodine
rate solution on a white tile. Initially, a strong blue–
10 20 30 40 50 60 black colour is seen confirming the presence
temperature at which the rate was measured/ºC
of starch. Later, as maltose accumulates, a red
denatured enzyme – colour forms. The end point of the reaction
enzyme in active state
substrate molecules is when all the starch colour has disappeared
no longer fit the active site from the test spot.
active site
▲ Figure 3.11 The effect of temperature on the rate of an enzyme-
catalysed reaction
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Using fresh reaction mixture each time, the investigation is repeated at a series of
different temperatures, say at 10, 20, 30, 40, 50 and 608C. The time taken for complete
hydrolysis at each temperature is recorded and the rate of hydrolysis in unit time
is plotted on a graph. A characteristic curve is the result – although the ‘optimum’
3
temperature varies from reaction to reaction and with different enzymes (Figure 3.11).
How is the graph interpreted? Look at Figure 3.11.
As the temperature is increased, molecules have more kinetic energy and reactions
between them happen more quickly. The enzyme molecules are moving more rapidly
and are more likely to collide and react. In chemical reactions, for every 108C rise in

temperature the rate of the reaction approximately doubles. This property is known as the
temperature coefficient (Q10) of a chemical reaction.
Question However, in enzyme-catalysed reactions the effect of temperature is more complex because
proteins are denatured by heat. The rate of denaturation increases at higher temperatures,
4 In studies of the
too. So as the temperature rises above a certain point the amount of active enzyme
effect of temperature
on enzyme-catalysed progressively decreases and the rate is slowed. As a result of these two effects of heat on
reactions, suggest enzyme-catalysed reactions, there is an apparent optimum temperature for an enzyme.
why the enzyme and Not all enzymes have the same optimum temperature. For example, the bacteria in hot
substrate solutions thermal springs have enzymes with optimum temperatures between 80 and 1008C or
are pre-incubated higher, whereas seaweeds of northern seas and the plants of the tundra have optimum
to a particular temperatures closer to 08C. Humans have enzymes with optimum temperatures at
temperature before or about normal body temperature. This feature of enzymes is often exploited in the
they are mixed. commercial and industrial uses of enzymes today.
pH
rate of enzyme-catalysed reaction
Change in pH can have a dramatic effect on

or amount of product formed
(amount of substrate used up
the rate of an enzyme-catalysed reaction. Each

enzyme has a range of pH in which it functions
per unit time)
efficiently – often at or close to neutrality. The pH

affects the rate of reaction because the structure
of a protein (and therefore the shape of the active
site) is maintained by various bonds within
the three-dimensional structure of the protein
(Figure 2.22, page 51). A change in pH from
the optimum value alters the bonding patterns.
As a result, the shape of the enzyme molecule
lower pH optimum pH for enzyme higher pH is progressively changed. The active site may
quickly become inactive. However, the effects
of pH on the active site are normally reversible
substrate molecules enzyme in substrate molecules
no longer fit the active state no longer fit the (unlike temperature changes). That is, provided
active site active site the change in surrounding acidity or alkalinity
is not too extreme. As the pH is brought back to
the optimum for that enzyme, the active site may
reappear (Figure 3.12).
Some of the digestive enzymes of the gut have
active site
different optimum pH values from the majority of
structure of protein changes when a change of pH alters the other enzymes. For example, those adapted to work
ionic charge on —COO–(acidic) and —NH3+ (basic) groups in the in the stomach, where there is a high concentration
peptide chain, so the shape of the active site is lost of acid during digestion, have an optimum pH
▲ Figure 3.12 The effect of pH on enzyme shape and activity which is close to pH 2.0 (Figure 3.13 overleaf).
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optimum pH of
most enzymes
3
optimum pH
of pepsin in human cells
(active in
acidic
rate of reaction
stomach) optimum pH
of trypsin
(active in neutral/
alkaline duodenum and
small intestine)
Question
3 Enzymes
5 a Explain what a
buffer solution is.
b Why are they
2 4 6 8 10
often used pH
in enzyme
experiments? ▲ Figure 3.13 The optimum pH of different human enzymes
Substrate concentration
The effect of different concentrations of substrate on the rate of an enzyme-catalysed
reaction can be shown using the enzyme catalase.
Look again at the investigation of the initial rate of reaction using catalase (Figure 3.8).
We saw that, when working with catalase, it is easy to measure the rate the product
(oxygen) accumulated (recorded at half minute intervals).
To investigate the effect of substrate concentration on the rate of this enzyme-catalysed
reaction, the experiment shown in Figure 3.8 is repeated at different concentrations
of substrate. The initial rate of reaction plotted in each case. Other variables such as
temperature and enzyme concentration are kept constant.
When the initial rates of reaction are plotted against the substrate concentration, the
curve shows two phases. At lower concentrations the rate increases in direct proportion
to the substrate concentration but at higher substrate concentrations, the rate of reaction
becomes constant and shows no increase (Figure 3.14).
We can see that the enzyme catalase does work by forming a short-lived enzyme–substrate
complex. At low concentrations of substrate, all molecules can find an active site without
delay. Effectively, there is excess enzyme present. The rate of reaction is set by how much
substrate is present – as more substrate is made available the rate of reaction increases.
At higher substrate concentrations there are more substrate molecules than enzyme
molecules. Now, in effect, substrate molecules have to ‘queue up’ for access to an active
site. Adding more substrate increases the number of molecules awaiting contact with
an enzyme molecule. There is now no increase in the rate of reaction. This relationship
between amount of substrate and the rate of reaction is shown in Figure 3.14.
Question 6 When there is an excess of substrate present in an enzyme-catalysed reaction,

explain the effects on the rate of reaction of increasing the concentration of:
a the substrate
b the enzyme.
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3
few substrate molecules, more substrate molecules, excess of substrate molecules,

many active sites free: all active sites engaged in catalysis: all active sites engaged in catalysis:

increase in substrate concentration maximum rate of reaction increase in substrate concentration
will increase the rate will not change the rate
high
initial rate of reaction
low
low high
substrate concentration
▲ Figure 3.14 The effect of substrate concentration on the rate of an enzyme-catalysed reaction
Enzyme concentration
If there are plenty of substrate molecules in a reaction mixture, then the more enzyme
that is added the faster the rate of reaction will be. This is the situation in a cell where
an enzyme reaction occurs with a small amount of enzyme present. Any increase in
enzyme production will lead to an increased rate of reaction, simply because more active
sites are made available.
Introducing the Michaelis–Menten constant (Km) and its

significance
On page 68 we saw how the initial rate of an enzyme-catalysed reaction was measured
and why (Figure 3.8).
Remind yourself ‘how’ and ‘why’ now.
When the initial rate of reaction of an enzyme is measured over a range of substrate
concentrations (with a fixed amount of enzyme) and the results plotted on a graph, a
typical example of the resulting curve is shown in Figure 3.15 (overleaf). You can see
that, with increasing substrate concentration, the velocity increases – rapidly at lower
substrate concentrations. However, the rate increase progressively slows, and above a
certain substrate concentration, the curve has flattened out. No further increase in rate
occurs. This tells us the enzyme is working at maximum velocity at this point. On the
graph, this point of maximum velocity is shown as Vmax.
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Vmax

1
V
2 max
Km
3 Enzymes
▲ Figure 3.15 Graph of initial rate of an enzyme-catalysed reaction against substrate

concentration
In 1913 the biochemists Michaelis and Menten studied this aspect of enzyme reactions
and introduced a constant, now known as the Michaelis–Menten constant. The
Michaelis–Menten constant (K m) is defined as the substrate concentration that
sustains half maximum velocity ( 12 Vmax). It measures the degree of attraction or affinity
of an enzyme for the substrate – the smaller the K m the higher the affinity. K m can be
experimentally determined at a specified pH and temperature, and is expressed in units
of molarity.
Actual values of K m have been measured for a great many enzymes. These values fall
between 10 −3 and 10 −5 mol dm3 of substrate. This is a very wide range of concentrations.
It means that some enzymes are able to work at maximum velocity at very low
concentrations of substrate, while others only function effectively at much higher
concentrations.
Take the case of two enzymes that catalyse the transformation of the same substrate
molecule but in different reaction sequences. If the ‘pool’ or reserves of that substrate are
low and its supply restricted, then the enzyme with the lowest K m will claim more – and
one particular metabolic pathway will benefit at the expense of the other. Knowing the
K m of enzymes is an important part of understanding metabolism, both quantitatively
and qualitatively.
Inhibitors of enzymes
Certain substances present in cells (and some which enter from the environment) may
react with an enzyme, altering the rate of reaction. These substances are known as
inhibitors, since their effect is generally to lower the rate of reaction. Studies of the
effects of inhibitors have helped our understanding of:
» the chemistry of the active site of enzymes
» the natural regulation of metabolism and which pathways operate
» the ways certain commercial pesticides and many drugs work (by inhibiting specific
enzymes and preventing particular reactions).
For example, molecules that sufficiently resemble the substrate in shape may compete
to occupy the active site. They are known as competitive inhibitors. For example, the
enzyme that catalyses the reaction between carbon dioxide and the CO2-acceptor molecule
in photosynthesis, known as ribulose bisphosphate carboxylase (rubisco), is competitively
inhibited by oxygen in the chloroplasts.
Because these inhibitors are not acted on by the enzyme and turned into ‘products’
as normal substrate molecular are, they tend to remain attached. However, if
the concentration of the substrate molecule is raised, the inhibitor molecules are
progressively displaced from the active sites (Figure 3.16).
Alternatively, an inhibitor may be unlike the substrate molecule, yet still combine with
the enzyme. In these cases, the attachment occurs at some other part of the enzyme.
This may be quite close to the active site. Here the inhibitor either partly blocks access
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When the initial rates of reaction of an enzyme are plotted against
substrate concentration, the effects of competitive and non-competitive
inhibitors are seen to be different.
3
substrate
maximum rate
of enzyme-catalysed reaction
without any inhibitor
active site
enzyme
effect of a competitive

inhibitor:
substrate and inhibitor
compete for active sites, so

competitive inhibitor change
excess substrate overcomes
in place: substrate prevented in shape
inhibition
from binding of active
site
two types of reversible
inhibition effect of a non-competitive
inhibitor:
inhibitor does not compete for
active sites, so excess substrate
will not overcome inhibition
non-competitive inhibitor
in place: catalytic activity of
active site prevented low high
▲ Figure 3.16 The principles of competitive and non-competitive inhibition
to the active site by substrate molecules or it causes the active site to change shape so
that it is then unable to accept the substrate.
These are called non-competitive inhibitors, since they do not compete for the active site.
Adding excess substrate does not overcome their inhibiting effects (Figure 3.16). An example
is the effect of the amino acid alanine on the enzyme pyruvate kinase in the final step of
glycolysis (Topic 12).
Competitive inhibition Non-competitive inhibition

Inhibitor chemically resembles the substrate Inhibitor chemically unlike the substrate
molecule and occupies (blocks) the active molecule but reacts with the bulk of the
site enzyme, reducing access to the active site
With a low concentration of inhibitor, With a low concentration of inhibitor,
increasing concentration of substrate increasing concentration of substrate
eventually overcomes inhibition as substrate cannot prevent binding of inhibitor –
molecules displace inhibitor some inhibition remains at high substrate
concentration
Example: Example:
O2 competes with CO2 for active site of alanine non-competitively inhibits pyruvate
rubisco kinase
▲ Table 3.1 A comparison of competitive and non-competitive inhibition of enzymes
Certain irreversible inhibitors bind tightly and permanently to an enzyme and destroy
its catalytic properties entirely. These drastic effects occur at low concentrations of
inhibitor and we may describe these substances as poisons. Examples include:
» cyanide ions which block cytochrome oxidase in terminal oxidation in cell aerobic
respiration
» the nerve gas sarin blocks a neurotransmitter (acetyl cholinesterase) in synapse
transmission.
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Use of enzymes as industrial and laboratory catalysts
3 Enzymes as biological catalysts are important components of many industrial processes.
Their use is widespread because they are:
» highly specific, catalysing changes in one particular compound or one type of bond
» efficient, in that a tiny quantity of enzyme catalyses the production of a large
quantity of product
» effective at normal temperatures and pressures, and so a limited input of energy
(as heat and high pressure) may be required.
3 Enzymes
The enzymes selected by industry are frequently produced from microorganisms –

typically from species of fungi or bacteria. Table 3.2 lists some examples.
Enzyme Source Application

Bacterial Protease Bacillus ‘Biological’ detergents
Glucose Bacillus Fructose syrup manufacture
isomerase
Fungal Lactase Kluyveromyces Breakdown of lactose to glucose and
galactose
Amylase Aspergillus Removal of starch in woven cloth
production
▲ Table 3.2 Enzymes with industrial applications obtained from microorganisms
Using enzymes in vitro

Enzymes may be used as cell-free preparations added to a reaction mixture, or they may
be immobilised enzymes, with the reactants passed over them.
Enzyme immobilisation involves the attachment of enzymes to insoluble materials,
which then provide support for the enzyme. For example, the enzyme may be entrapped
between inert fibres, or it may be covalently bonded to a matrix. In both cases the
enzyme molecules are prevented from being leached away. The immediate advantages of
using an immobilised enzyme are:
» it permits re-use of the enzyme preparation
» the product is obtained enzyme free
» the enzyme may be much more stable and long lasting, due to protection by the inert
matrix.
Clearly, there are advantages in using industrial enzymes in the immobilised condition,
where this is possible. We will return to this issue shortly. First, we can investigate the
process of immobilisation of an enzyme and compare its activity when alternatively used
free in a solution.
Immobilised enzyme – a laboratory demonstration

The steps to this demonstration are:
1 A solution of sodium alginate (a polysaccharide obtained from the walls of brown
algae, capable of holding 200 times its own mass in water) is prepared by dispersing
2 g of the alginate in 100 cm3 of distilled water at a temperature of 40 °C.
2 An alginate-enzyme solution is prepared by stirring 2 cm3 of invertase concentrate
into 40 cm3 of the cooled alginate solution. (Remember, invertase catalyses the
hydrolysis of sucrose [a disaccharide] to two monosaccharide molecules [glucose and
fructose] from which it is formed in a condensation reaction.)
3 Immobilised enzyme pellets are produced by filling a syringe with the alginate-
invertase solution and arranging for it to drip into a beaker of calcium chloride
solution (100 cm3 of CaCl2, 0.1 mol dm3). The insoluble pellets formed may be
separated with a nylon/plastic sieve. They should be washed with distilled water at
this stage, and allowed to harden.
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Preparing immobilised enzyme in alginates Harvesting alginate-enzyme beads Using immobilised enzyme beads
3
beads formed are hardened beads enzyme substrate
harvested in a are transferred solution (sucrose)
syringe nylon sieve to a tube is poured in
substrate solution
alginate-enzyme washed with trickles slowly past
(invertase) solution distilled water the beads
dripped into calcium

chloride solution narrow
nozzle
beaker
products of the
enzyme reaction
(glucose + fructose solution)
▲ Figure 3.17 Preparing an immobilised enzyme
4 These hardened pellets may be tested by placing them in a tube with a narrow
nozzle at the base (the barrel of a large, plastic syringe is suitable). A quantity of
sucrose solution (30 cm3 of 5% sucrose w/v) may be slowly poured down the column
of pellets and the effluent collected. Note the time taken for the solution to pass
through.
5 Test the effluent solution for the presence of glucose, using Clinistix™ (see below).
Investigating the efficiency of immobilised enzyme compared

to its use free in solution
A comparison of the efficiency of immobilised invertase compared with free enzyme
can be made by stirring into a second sample of the sucrose solution (again, 30 cm3 of
5% sucrose w/v), 2 cm3 of the invertase concentrate solution. The free enzyme should
be allowed to catalyse hydrolysis of the sucrose for the same time period as it took for
the earlier sucrose solution sample to pass through the alginate bead column. Once
again, the solution should be tested for the presence of glucose, using ClinistixTM (see
Figure 3.18, overleaf).
Estimating the glucose concentration using ClinistixTM

ClinistixTM exploit immobilised enzymes in dipsticks for the quantitative measurement
of glucose. (An important medical application of the ClinistixTM has been the
measurement of glucose in urine samples in patients with diabetes.)
The ClinistixTM strip contains two enzymes, glucose oxidase and peroxidase, together
with a colourless hydrogen donor compound called chromogen. When the strip is
dipped into a sample, if glucose is present it is oxidised to glucuronic acid and hydrogen
peroxide. The second enzyme catalyses the reduction of hydrogen peroxide and the
oxidation of chromogen. The product is water and the oxidised dye, which is coloured.
The more glucose present in the sample the more coloured dye is formed. The colour
of the test strip is then compared to the printed scale to indicate the amount of glucose
present (Figure 3.18).
Note that this is another example of the industrial exploitation of biological catalysts.
How effective was the immobilised enzyme, compared to its activity, free in solution?
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the principles
glucose oxidase
3 glucose + oxygen gluconic acid + H2O2
peroxidase
DH2 + H2O2 2H2O + D
reduced chromagen
chromagen (coloured)
(colourless)
3 Enzymes
the process
test strip dipped

into sample solution
▲ Figure 3.18 Measuring glucose in urine using a Clinistix™
What are the advantages and disadvantages of immobilisation?

The most obvious advantage is the recovery of the enzyme and its availability for re-use.
Other issues are listed in Table 3.3.
Advantages Disadvantages
The enzyme is held in a form that can be manipulated An immobilisation mechanism that does not alter the shape
easily. It is absent from the product, so no purification or the catalytic ability of the enzyme must be selected.
steps are required.
The enzyme is available for multiple re-use, since it The creation of stable, hardened pellets is an added
functions as an effective catalyst in pellet form. expense that is inevitably reflected in the cost of the
industrial product.
An immobilised enzyme is stable at the temperatures and If the enzyme becomes detached it will appear in the
pH at which it is held and used. product as a contaminant, possibly unnoticed.
▲ Table 3.3 Advantages and disadvantages of immobilisation
SUMMARY
» Metabolism, all the chemical reactions of life, molecule to a transition state (the induced fit
consists of anabolic reactions, the build up of hypothesis), from which the products may form.
complex molecules from smaller ones, e.g. The enzyme is released for reuse.
protein synthesis, and catabolic reactions, the » The rate of an enzyme-catalysed reaction is found
breakdown of complex molecules, e.g. oxidation of by measuring the disappearance of the substrate
sugar in respiration. or the accumulation of the product in a given
» All reactions of metabolism are made possible period of time. The initial rate of reaction is taken
by enzymes. Enzymes are biological catalysts and since the reaction rate falls with time under
most are made of globular protein. An enzyme is experimental conditions.
highly specific to the type(s) of substrate molecule » A colorimeter can be used to measure the rate of
and type of reaction that they catalyse. enzyme-catalysed reactions that involve a colour
» Enzymes work by forming a temporary complex change.
with a substrate molecule at a special part of the » The factors that affect the rate of an enzyme-
enzyme surface, called the active site (the lock- catalysed reaction include pH and temperature –
and-key hypothesis). Enzymes work by lowering through their effects on protein structure. When
the activation energy needed for a reaction to molecules of substances recognised as inhibitors
occur. are in contact with enzyme molecules, the rate of
» A slight change in shape of the substrate molecule reaction may be lowered in characteristic ways.
when it binds to the active site helps raise the
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» The Michaelis–Menten constant (Km) is the » Industries use enzymes as biological catalysts,
substrate concentration that sustains half
maximum velocity ( 12 Vmax) of an enzyme-catalysed
often immobilised, with the reactants passed
over them. In these cases, the advantages are the 3
reaction. It is a measure of the degree of affinity of recovery of the enzyme and its availability for re-
an enzyme for its substrate. Km can be measured use. Being immobilised may affect the enzyme’s
experimentally, and is expressed in units of efficiency compared to use of the same enzyme
molarity. Values of Km have been measured for when free in the substrate solution.
a great many enzymes, and it has been shown
that some enzymes are able to work at maximum

velocity at very low concentrations of substrate.

1 The enzyme sucrase catalyses the breakdown of the glycosidic bond in sucrose.
A student investigated the effect of increasing the concentration of sucrose on the
rate of activity of sucrase.
Ten test-tubes were set up with each containing 5 cm3 of different concentrations
of a sucrose solution. The test-tubes were placed in a water bath at 408C for ten
minutes. A flask containing a sucrase solution was also put into the water bath.
After ten minutes, 1 cm3 of the sucrase solution was added to each test-tube. The
reaction mixtures were kept at 408C for a further ten minutes.
After ten minutes, the temperature of the water bath was raised to boiling point.
Benedict’s solution was added to each test-tube. The time taken for a colour
change was recorded and used to calculate rates of enzyme activity.
The results are shown in Fig. 1.1.
12
rate of enzyme activity/arbitrary units
10
0
0 20 40 60 80 100
concentration of sucrose/g dm–3
▲ Fig. 1.1
a i Name the type of reaction catalysed by sucrase. [1]

ii Explain why the temperature of the water was raised to boiling point. [2]
b Describe and explain the results shown in Fig. 1.1. [5]
[Total: 8]
(Cambridge International AS and A Level Biology 9700 Paper 21 Q4 May/June 2011)
2 Statements A to E are about the structure and functioning of enzymes.
State the correct term to match each of the statements A to E.
A The energy level, lowered by enzyme action, that needs to be overcome by
reactants in order for products to be formed.
B The mechanism of enzyme action that relies on the active site being partially
flexible and changing shape in order to bind the substrate.
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C The term to describe a protein, such as an enzyme, with a tertiary or
quaternary structure that results in an approximately spherical shape.
3 D The term for enzymes that function outside cells.
E The concentration of substrate that enables an enzyme to achieve half the
maximum rate of reaction. [5]
[Total: 5]
3 a Explain how enzymes lower the activation energy needed to allow reactions
to proceed. [2]
3 Enzymes
b Folic acid is a molecule used by all cells for growth. Bacteria cannot absorb
folic acid from their surroundings. Bacteria use an enzyme to make a molecule
called PABA. PABA is used to make folic acid.
An investigation was carried out to determine the effect on the production
of PABA when the concentration of an enzyme inhibitor is increased. Four
different concentrations (1 μM to 30 μM) of the inhibitor were used, together
with a control with no inhibitor.
The concentration of PABA produced in each reaction mixture was determined
at 10-minute intervals.
The results are shown in Fig. 3.1.
concentrations
5
of inhibitor
no inhibitor
1μM
4
concentration of PABA produced / μM
3 μM
3
10 μM
2
30 μM
1
0
0 10 20 30 40 50 60
time / min
▲ Fig. 3.1
i Use Fig. 3.1 to describe the results of the investigation. [4]

ii Outline an experiment that could be carried out to determine whether the
inhibitor of the enzyme that catalyses the reaction to produce PABA is
competitive or non-competitive. [3]
[Total: 9]
(Cambridge International AS and A Level Biology 9700 Paper 23 Q2 a, b(i, ii) Oct/Nov 2016)
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AS LEVEL
4.1 Fluid mosaic membranes

The fluid mosaic model, Learning outcomes
introduced in 1972,
describes the way in which By the end of this topic, you will be able to:
biological molecules are 4.1.1 describe the fluid mosaic model of membrane structure with reference
arranged to form cell to the hydrophobic and hydrophilic interactions that account for the
membranes. The model formation of the phospholipid bilayer and the arrangement of proteins
continues to be modified 4.1.2 describe the arrangement of cholesterol, glycolipids and glycoproteins in
as understanding improves cell surface membranes
of the ways in which
substances cross membranes,
4.1.3 describe the roles of phospholipids, cholesterol, glycolipids, proteins
how cells interact and how and glycoproteins in cell surface membranes, with reference to stability,
cells respond to signals. fluidity, permeability, transport (carrier proteins and channel proteins),
The model also provides the cell signalling (cell surface receptors) and cell recognition (cell surface
basis for our understanding antigens – see 11.1.2)
of passive and active 4.1.4 outline the main stages in the process of cell signalling leading to specific
movement of molecules and responses: secretion of specific chemicals (ligands) from cells, transport
ions between cells and their of ligands to target cells and binding of ligands to cell surface receptors
surroundings, cell-to-cell
on target cells
interactions and long-
distance cell signalling.
Investigating the effects Starting point
of different factors on
★ The structure of cell surface membranes allows movement of substances
diffusion, osmosis and
membrane permeability between cells and their surroundings and allows cells to communicate with
involves an understanding each other by cell signalling.
of the properties of
phospholipids and proteins
covered in Biological
molecules (Topic 2).
The cell surface membrane
An organelle with many roles
The cell surface membrane is an organelle common to both eukaryotic and prokaryotic
cells. It is an extremely thin structure, less than 10 nm thick, yet it has the strength to
maintain the integrity of the cell. In addition to holding the cell’s contents together, the
cell surface membrane forms the barrier across which all substances entering or leaving
the cell must pass. This membrane represents the ‘identity’ of the cell to surrounding
cells. It is also the surface across which chemical messages (such as hormones and growth
factors) communicate. In fact, movement of molecules across the cell surface membrane is
continuous and very heavy. Figure 4.1 overleaf is a summary of all this membrane traffic.
Composition of the membrane and control of how fluid it is

The phospholipids of the membrane are a mixture. Some have saturated fatty acid tails
and some unsaturated fatty acid tails (Figure 2.16, page 45). An excess of unsaturated
fatty acid tails makes the membrane more fluid. This is because the kinks in the tails
prevent close-packing of the lipids. However, the presence of cholesterol among the
phospholipid molecules has to be taken into account. The effect of cholesterol is to
reduce fluidity by preventing or reducing the movements of the lipid molecules.
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Membrane fluidity is an important factor. Membranes must be sufficiently fluid
for many of the proteins present to move about and so to function correctly. If the
4 temperature of a membrane falls it becomes less fluid. A point may be reached when the
membrane will actually solidify. Some organisms have been found to vary the balance
between saturated and unsaturated fatty acids and the amount of cholesterol in their
membranes as ambient temperatures changes. In this way they maintain a properly
functioning membrane, even at very low temperatures, for example.
water uptake/loss secretion
neurotransmitter substances
H 2O hormones
enzymes procollagen
(assembled into
collagen fibres
respiration outside the
mammalian cell)
O2
CO2 cell wall
components –
cellulose and
hemicellulose
(assembled to
make plant cell
wall, outside cell)
nutrition
sugars excretion
amino acids ions NH 3
fatty acids
e.g. Na+, K+, Ca2+, also urea
vitamins (animals)
trace elements (e.g. Fe, Cu)
▲ Figure 4.1 The movement of substances across the cell surface membrane
The molecular components of membranes

The membranes of cells are made almost entirely of protein and lipid, together with a
small and variable amount of carbohydrate. The lipid of membranes is phospholipids
and cholesterol. The chemical structure of phospholipids is shown in Figure 2.18 on
a phospholipid molecule has
page 46.
a hydrophobic tail – which
repels water – and a Look at its structure again now.
hydrophilic head – which
attracts water You can see that the phospholipid molecule has a ‘head’ composed of a glycerol to which
is attached an ionised phosphate group. This latter part of the molecule has hydrophilic
Phospholipid molecules in contact properties (water-loving). For example, hydrogen bonds readily form between the
with water form a monolayer,
with heads dissolved in the water
phosphate head and water molecules. The remainder of the phospholipid comprises
and the tails sticking outwards. two long, fatty acid residues consisting of hydrocarbon chains. These ‘tails’ have
hydrophobic properties (water-hating).
water The response of phospholipid to water
A small quantity of phospholipid in contact with a solid surface (a clean glass plate
is suitable), remains as a discreet bubble; the phospholipid molecules do not spread.
When mixed with water, However, when a similar tiny drop of phospholipid is added to water it instantly
phospholipid molecules arrange spreads over the entire surface (as a monolayer of phospholipid molecules, in fact).
themselves into a bilayer, in
which the hydrophobic tails are
The molecules float with their hydrophilic ‘heads’ in contact with the water molecules,
attracted to each other. and with their hydrocarbon tails exposed above and away from the water, forming a
monolayer of phospholipid molecules (Figure 4.2).
When more phospholipid is added, the phospholipid molecules may arrange themselves
water as a bilayer, again with the hydrocarbon tails facing together (Figure 4.2). This is how
the molecules of phospholipid are arranged in the cell surface membrane.
▲ Figure 4.2 Phospholipid In the phospholipid bilayer, attractions between the hydrophobic hydrocarbon tails on
molecules arranged in a the inside and between the hydrophilic glycerol–phosphate heads and the surrounding
monolayer and a bilayer water on the outside make a stable, strong barrier.
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The permeability of a phospholipid membrane
We must note, however, that while lipids provide a cohesive structure, they also tend
to act as a barrier to the passage of polar molecules and ions. This is particularly the 4
case where close-packing of the hydrocarbon tails occurs. Potentially, water-soluble
substances pass through the lipid bilayer with great difficulty. We will return to this
issue shortly, too.
The fluid mosaic model of membrane structure

The molecular structure of the cell surface membrane, known as the fluid mosaic model

by those who first suggested it, is shown in Figure 4.3. The membrane they described as
fluid because the components (lipids and proteins) move around within their layer. In fact
the movements of the lipid molecules are rapid, whereas mobile proteins move about more
slowly. The word mosaic described the scattered pattern of the proteins, when viewed from
above. This is the current view of the structure of the cell surface membrane. It is based on
a range of evidence, in part from studies with the electron microscope (Figure 4.4).
three-dimensional view peripheral proteins –
polysaccharide glycoprotein attached to surface of lipid bilayer
outside of cell protein
polysaccharide
glycolipid
lipid
lipid
bilayer
protein that traverses

the membrane, and
is exposed at both
surfaces channel protein
with pore
cholesterol
diagrammatic cross-sectional view protein on one
side of the integral proteins –
membrane embedded in the lipid bilayer
inside of cell
▲ Figure 4.3 The fluid mosaic model of membrane structure
TEM of the cell surface membrane of a electron micrograph of the cell

red blood cell (×700 000) cell surface membrane in cross-section membrane (freeze-etched)
polysaccharides
lipid bilayer inner
surface
interior of cell of lipid
bilayer
lipid bilayer protein

inner face of molecules
membrane line of fracture of
membrane shown
to the right
▲ Figure 4.4 Membrane structure: evidence from the electron microscope

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Questions 1 In plants adapted to survive in very low winter temperatures, what seasonal change
4 would you anticipate in the composition of the lipid bilayer of their membranes?
2 What is the difference between a lipid bilayer and the ‘double membrane’ of many
organelles?
Proteins, carbohydrates and cholesterol in cell surface membranes

The proteins of membranes are globular proteins, which are buried in and across the
lipid bilayer, with most projecting above the surfaces. Others are superficially attached
on either surface of the lipid bilayer.
Proteins that occur partially or fully buried in the lipid bilayer are described as integral
proteins. Those that are superficially attached on either surface of the lipid bilayers are
known as peripheral proteins.
Membrane proteins have a range of roles. Some are enzymes, others are receptors, or
antigens, and many are channels for transport of metabolites. Those that are involved
in transport of molecules across membranes are in the spotlight in the next section. A
summary of the various roles of membrane proteins is given in Figure 4.26 (page 102),
after the movements of molecules across the membrane have been discussed.
The carbohydrate molecules of the cell surface membrane are relatively short chain
polysaccharides, some attached to the proteins (glycoproteins) and some to the lipids
(glycolipids) Glycoproteins and glycolipids are only found on the outer surface of the
membrane.
Glycoproteins act as receptor sites for chemical signals, such as hormone messengers;
they are also important for cell–cell recognition and assist in the binding together of
cells to form tissues.
Glycolipids help to maintain the stability of the cell membrane as well as facilitate
cell–cell recognition.
Finally, the phospholipid bilayer has been found to contain molecules of cholesterol.
Cholesterol is an essential component of cell membranes, embedded in the hydrophobic
areas of the inner (tail) region. Its large structure hinders the regular packing of
phospholipids. This has the effect of reducing membrane fluidity at moderate
temperatures but preventing the membrane from solidifying at low temperatures.
Cholesterol also limits uncontrolled leakage of small molecules such as water and ions in
and out of the membranes.
The cell surface membrane and cell signalling

Cells respond to changes in their environment by receiving and integrating signals from
other cells. They also send out messages. Most cell signals are chemical signals (ligands).
For example, motile single-celled organisms detect nutrients in their environment and
move towards the source. In multicellular organisms, chemical signals include growth
factors and hormones that may have come from neighbouring cells or from more distant
sources. Neurotransmitters cross a tiny gap from a neighbouring nerve cell and transmit a
signal (page 328).
Cells are able to detect these signals because of receptors in their cell surface membrane to
which the ‘chemical message’ binds, and then trigger an internal response. Receptors are
typically trans-membrane proteins, which on receipt of the signal, alert internal signalling
pathways. Embedded in the plasma membrane are specifically shaped receptor extrinsic
proteins, which are attachment sites for ligands with the complementary shape. Receptor
proteins work to regulate the biological function of individual cells, enabling cells, tissues
and organs to sense and respond to their environment and even influence other cells by
sending out chemical messengers that interact with the receptors on those cells.
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Lipid-insoluble ligands cannot diffuse through the plasma membrane of cells. They
bind to receptors on the outer surface of the plasma membrane and this binding
initiates reactions inside the cell (Figure 4.5a). When the chemical message arrives at
its final destination, a specific action occurs. For example, the cell may divide, or it
4
may be instructed to increase or decrease the expression of particular genes, metabolise
chemicals such as glucose into energy for the cell, or turn genes on or off. When
adrenalin binds to adrenalin receptors, it triggers a cascade of reactions within the cells
that result in the release of glucose from the cell.
Many lipid-soluble ligands diffuse across the plasma membrane, diffuse into the

nucleus, bind to the DNA and initiate specific protein synthesis, which then initiates
reactions (Figure 4.5b). Steroid hormones such as oestrogen, progesterone and
testosterone are examples of this sort of ligand.
a) lipid-insoluble ligand b) lipid-soluble ligand
target cell
target cell
receptor protein
receptor product protein synthesis
protein
activated enzyme
ligand-receptor
or other protein DNA
complex
mRNA
secondary messengers nucleus
▲ Figure 4.5
Some intrinsic proteins have pores in the centre (channel proteins) which allow
transport of substances that would otherwise not be able to cross the membranes. Some
hydrophilic protein channels are permanently open, such as those that enable the rapid
transport of water molecules. These are known as aquaporins (see page 310).
Some of the most common migrants across the plasma membrane are charged ions such
as sodium, potassium, chloride and calcium. Protein channels and pumps embedded
in the plasma membrane regulate the flow of charged particles across the membrane.
By allowing ions of specific charge to move in or out, they change the membrane
permeability. For example, in nerve cells, voltage-gated channels transport sodium and
potassium ions across the nerve cell membrane in response to stimuli (page 99).
Cotransporter proteins take part in a particular type of transport called facilitated
diffusion (see page 90) that couples the transport of an ion (e.g. Na1, H1) down
its concentration gradient with a second solute against the concentration gradient.
Glucose and amino acids are cotransported with sodium ions in the kidney in this way
(Figure 4.6). After binding of the polar molecule to the binding site, the carrier protein
changes shape and transfers the molecule to the other side of the membrane.
extracellular
fluid Na+ concentration is higher Na+ is transported down
glucose on this side of the membrane its concentration gradient
Na+
cytoplasm cotransporter glucose concentration is

proteins higher on this side of the glucose is transported
hydrophilic region membrane up its concentration
hydrophobic region gradient
▲ Figure 4.6
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Summarising the role of membrane proteins in cells
4 The many roles that cell membrane proteins play (as channels for transport of
metabolites, as pumps for active transport, as electron carriers, carrier proteins, cells
surface receptors, and as binding sites for specific hormone molecules and in antigen–
antibody reactions) are outlined in Figure 4.26 on page 102.
Look at this diagram now.
The potential for complex communications between cells that may result as chemicals
released from one cells combine with cell surface receptors on neighbouring cells is
evident. It is the proteins of cell surface membranes that facilitate this ‘cell signalling’.
4.2 Movement into and out of cells

Learning outcomes
4.2.1 describe and explain the processes of simple diffusion, facilitated
diffusion, osmosis, active transport, endocytosis and exocytosis
4.2.2 investigate simple diffusion and osmosis using plant tissue and non-living
materials, including dialysis (Visking) tubing and agar
4.2.3 illustrate the principle that surface area to volume ratios decrease with
increasing size by calculating surface areas and volumes of simple 3-D
shapes (as shown in the Mathematical requirements)
4.2.4 investigate the effect of changing surface area to volume ratio on diffusion
using agar blocks of different sizes
4.2.5 investigate the effects of immersing plant tissues in solutions of different
water potentials, using the results to estimate the water potential of the
tissues
4.2.6 explain the movement of water between cells and solutions in terms
of water potential and explain the different effects of the movement of
water on plant cells and animal cells (knowledge of solute potential and
pressure potential is not expected)
Starting points
★ The fluid mosaic model allows an understanding of how substances enter and
exit cells by a variety of different mechanisms.
★ Investigating the effect of increasing the size of model cells allows an
understanding of the constraints of obtaining resources across the cell
surface and moving substances out of cells.
Into and out of cells passes water, respiratory gases (O2 and CO2), nutrients, essential
mineral ions and excretory products. Cells may secrete substances such as hormones
and enzymes. They may receive growth substances and hormones, too. Plants secrete
the chemicals that make up their walls through their membranes, and assemble and
maintain the wall outside the membrane. Certain mammalian cells secrete structural
proteins such as collagen in a form that can be assembled outside the cells.
In addition, the membrane at the cell surface is where the cell is identified by
surrounding cells and organisms. For example, protein receptor sites are recognised by
hormones, neurotransmitter substances (from nerve cells), as well as other chemicals,
sent from other cells.
We will now look into the mechanisms of membrane transport. Figure 4.7 is a
summary of the mechanisms of transport across membranes.
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1 diffusion 4
movement from high to
low concentration; mitochondrion
energy source = kinetic
energy of molecules
ATP as energy
currency
osmosis 3 bulk transport
diffusion of water pump in transport of solids and/or

molecules across membrane liquids by vesicle at the
a membrane cell surface membrane;
energy source = energy
from metabolism
2 active transport
selective movement of substances,
against a concentration gradient;
energy source = energy from metabolism
▲ Figure 4.7 Mechanisms of movement across membranes
Movement by diffusion
The atoms, molecules and ions of liquids and gases undergo continuous random
movements. These movements result in the even distribution of the components of a
gas mixture and of the atoms, molecules and ions in a solution. This is why we are able
to take a tiny random sample from a solution and analyse it to find the concentration of
dissolved substances in the whole solution. Every sample has the same composition as
the whole. Similarly, every breath we take has the same amount of oxygen, nitrogen and
carbon dioxide as the atmosphere as a whole.
Continuous random movements of all molecules ensures complete mixing and even
distribution of molecules, given time, in solutions and gases. The energy for diffusion
comes from the kinetic energy of molecules. ‘Kinetic’ means that a particle has this
energy because it is in continuous motion.
Diffusion is the free passage of molecules (and atoms and ions) from a region of their
high concentration to a region of low concentration. Where a difference in concentration
has arisen in a gas or liquid, random movements carry molecules from a region of high
concentration to a region of low concentration. As a result, the particles become evenly
dispersed. The factors affecting the rate of diffusion are listed in Table 4.1.
The conditions needed to achieve rapid diffusion across

Factors affecting the rate of diffusion a surface
Concentration gradient – the greater the difference in A fresh supply of substance needs to reach the surface and
concentration between two regions, the greater the amount the substance that has crossed needs to be transported
that diffuses in a given time. away.
Distance over which diffusion occurs – the shorter the The structure needs to be thin.
distance, the greater the rate of diffusion.
Area across which diffusion occurs – the larger the area, the The surface area needs to be large.
greater the diffusion.
Structure through which diffusion occurs – pores or gaps in A greater number of pores and a larger size of pores may
structures may enhance diffusion. enhance diffusion.
Size and type of diffusing molecules – smaller molecules Oxygen may diffuse more rapidly than carbon dioxide.
and molecules soluble in the substance of a barrier will Fat-soluble substances diffuse more rapidly through the
both diffuse more rapidly. lipid bilayer than water-soluble substances.
▲ Table 4.1 Factors affecting the rate of diffusion
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Demonstrating diffusion
4 Diffusion in a liquid can be illustrated by adding a crystal of a coloured mineral to

distilled water. Even without stirring, the ions become evenly distributed throughout the
water. The process takes time, especially as the solid has first to dissolve (see Figure 4.8).
Cell surface : volume ratio, cell size and diffusion
As a cell grows and increases in size an important difference develops between the
surface area available for exchange by diffusion and the volume of the cytoplasm in
which the chemical reactions of life occur. The volume increases faster than surface area;
the surface area : volume ratio falls (see Figure 4.9). So, with increasing size of a cell, less
and less of the cytoplasm has access to the cell surface for exchange of gases, supply of
nutrients and loss of waste products.
Put another way, we can say that the smaller the cell is, the more quickly and easily
can materials be exchanged between its cytoplasm and environment by diffusion. One
consequence of this is that cells cannot continue growing larger, indefinitely. When a
maximum size is reached cell growth stops. The cell may then divide.
1 A crystal of potassium 2 As the ions dissolve, 3 The ions become evenly

permanganate (potassium random movements distributed. Random movements
manganate(VII), KMnO4) is disperse them through continue, but there is now no net
placed in distilled water. the water. movement in any particular direction.
water molecules
potassium ions
and permanganate
ions
▲ Figure 4.8 Diffusion in a liquid

cubic cell of increasing size
t
men
nv iron
nal e
ratio xter
A:V he e
g S s s to t
in cce
reas as a
dec ior h
t e r
in
e cell’s
f th
less o
s ively
gres
pro
1 mm 2 mm 3 mm 4 mm
dimensions/mm 1×1×1 2×2×2 3×3×3 4×4×4
surface area/mm2 6 24 54 96
volume/mm3 1 8 27 64
surface area : 6 24 54 96
6:1 = =6 24:8 = =3 54:27 = =2 96:64 = = 1.5
volume ratio 1 8 27 64
▲ Figure 4.9 The effect of increasing size on the surface area : volume ratio
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Question 3 For imaginary cubic ‘cells’ with sides 1, 2, 4 and 6 mm:
a calculate the volume, surface area and ratio of surface area to volume for each 4
b plot a graph of the surface area of these cells against their volume
c state the effect on the SA : V ratio of a cell as it increases in size
d explain the effect of increasing cell size on the efficiency of diffusion in the
removal of waste products from cell cytoplasm.
Demonstrating the connection between surface area : volume

ratio and diffusion
Working with a block of gelatine containing the acid-base indicator cresol red (coloured
red in alkali, yellow in acid), small, regular-shaped blocks of known dimension can be
cut, and then immersed in acid solution. The time taken for the red colour to completely
disappear can be recorded in a table, against the dimensions of the blocks, listed
in increasing size. The results of one such investigation are recorded in Question 4.
Examine the data there, and answer the questions that follow.
Question 4 Cubes of slightly alkaline gelatin of different dimensions, containing an acid–alkali

indicator (red in alkalis but yellow in acids) were prepared. The cubes were then
placed in dilute acid solution and the time taken for the colour in the gelatin to
change from red to yellow was measured.
Dimensions/mm Surface area/mm2 Volume/mm3 Time/minutes
10 3 10 3 10 600 1000 12
53535 150 125 4.5
2.5 3 2.5 3 2.5 37.5 15.6 4.0
a For each block, calculate the ratio of surface area to volume (SA/V).
b Explain why the colour changes more quickly in some blocks than others.
Diffusion in cells
Diffusion across the cell surface membrane (Figure 4.10) occurs where:
» the membrane is fully permeable to the substance concerned. The lipid bilayer of the
cell surface membrane is permeable to non-polar substances, including steroids and
glycerol, and also oxygen and carbon dioxide in solution, all of which diffuse quickly
via this route. Note that the net diffusion of different types of particle can take
place in opposite directions without hindrance, too. So, at the lung surface, oxygen
diffuses into the blood while carbon dioxide diffuses out.
polar molecules, e.g. water, in
molecules of a non-polar substance, high concentration
e.g. steroids, glycerol, fatty acids,
permanent pores in the cell
O2 and CO2 in solution
surface membrane
cell surface
membrane
diffusion between
the molecules of
the lipid bilayer
diffusion occurs in both directions, but there
is net movement from a region of high net diffusion of polar molecules to a region
concentration to a region of low concentration where they are in lower concentration
▲ Figure 4.10 Diffusion across the cell surface membrane
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» the pores in the membrane are large enough for a substance to pass through. Water
diffuses across the cell surface membrane by means of the protein-lined pores of
4 the membrane. The tiny spaces between the phospholipid molecules are another
route for water molecules. This latter occurs more easily where the fluid-mosaic
membrane contains phospholipids with unsaturated hydrocarbon tails, for here
these hydrocarbon tails are spaced more widely. In this state, the membrane is
consequently especially ‘leaky’ to water, for example.
Facilitated diffusion
In facilitated diffusion, a substance that otherwise is unable to diffuse across the cell
surface membrane does so. This is as a result of its effect on a particular protein in the
membrane. These are globular proteins that can form into pores large enough for diffusion.
Those pores close up again when that substance is no longer present (Figure 4.11).
substance X
triggers pore
to open
globular
protein in
lipid bilayer
temporary pores in
the membrane
diffusion of substance X from
region of high concentration
to region of low concentration
through specific pores
▲ Figure 4.11 Facilitated diffusion
Alternatively a channel protein may be selective. For example, some channel proteins
are ‘gated’ and open to allow the passage of ions only under particular conditions. There
are different channels for potassium ions and sodium ions in the membrane of nerve
fibres, for example (Figure 15.7, page 324).
Such proteins undergo rapid shape changes when in contact with a particular solute
molecule. Facilitated diffusion follows. The movement of glucose into red blood cells
occurs in this way. So does the movement of ADP into mitochondria and the movement
Question of ATP from mitochondria into the cytosol.
‘diffusion’ and Remember that in facilitated diffusion the energy comes from the kinetic energy of the
‘facilitated diffusion’. molecules involved, as is the case in all forms of diffusion. Energy from metabolism is
not required – it is a passive process.
Osmosis – a special case of diffusion

First, look at the experiment shown in Figure 4.12. The bag shown here is made from a short
length of dialysis tubing. Some sucrose solution is added, perhaps by using a small plastic
syringe. This is an experiment that is easy to set up. When this partially filled bag is
lowered into a beaker of water it quite quickly becomes stretched and turgid. Obviously
there is a huge inflow of water. This is a simple but dramatic demonstration of osmosis.
Why does osmosis happen? Remember, in a sucrose solution the sucrose molecules are
the solute and the water molecules are the solvent.
a solution 5 solute 1 solvent
We saw in Topic 2 that in a solution, a dissolved substance attracts polar water
molecules around it (Figure 2.28, page 57). The forces holding those water molecules in
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this way are hydrogen bonds. The effect of the presence of a ‘cloud’ of water molecules
around each solute molecule is to hamper and restrict their movements. Organic
substances like sugars, amino acids, polypeptides and proteins, and inorganic ions like
4
Na1, K1, Cl2 and NO32, all have this effect on the water molecules around them. On the
other hand, in pure water, all of the water molecules are free to move about randomly,
and do so – all the time. We say that here they diffuse freely.
In the experiment in Figure 4.12, the solution of sugar was separated from pure water
by a membrane – the walls of a dialysis tube. This is described as partially permeable

because it only allows certain molecules to pass, not all of them. Water molecules move
across the membrane in both directions, by diffusion. At the same time, the solute
molecules with their cloud of water molecules are too large to pass through. In the mean
time, there is a continuing net movement of water molecules from the region of high
concentration of free water molecules (the molecules of pure water in the beaker) to the
region of low concentration of free water molecules (the water molecules of the sucrose
solution). This causes the bag to fill up and become stretched and turgid.
Water potential
The name given to the tendency of water molecules to move about is water potential.
‘Water potential’ is really a measure of the free kinetic energy of the water molecules.
The Greek letter psi (symbol ψ) is used to represent water potential.
Water moves from a region of higher water potential to a region of lower water potential.
We say water moves down a water potential gradient. Equilibrium is reached only if
or when the water potential is the same in both regions. At this point, there would be
no net movement of water from one region to another, but random movements of water
molecules continue, of course.
1 A bag made from dialysis 2 The bag is lowered This experiment can be
tubing, containing a into water. carried out in your laboratory.
concentrated solution
of sucrose.
distilled
water
3 Water enters the bag,

which becomes
stretched.
dialysis tube – a partially dialysis tube with

permeable membrane sucrose solution
slow-moving sucrose molecules

net flow with attached water molecules – few escape from
of water the bag into the surrounding water
into the bag
volume of the bag has

increased, due to
water uptake
water molecules
water molecules
free to move about
attracted to sucrose molecules
▲ Figure 4.12 Osmosis
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Questions 6 What is meant when we say a membrane is partially permeable?
4 7 When a concentrated solution of glucose is separated from a dilute solution of
glucose by a partially permeable membrane, which solution will show a net gain of
water molecules? Why do we speak of a ‘net’ gain?
8 Jam is made of equal weights of fruit and sucrose. What happens to a fungal spore
that germinates after landing on jam?
The concentration of solute molecules and water potential

Pure water obviously has the highest water potential. By convention, this is set at zero.
Once a solute is dissolved in water, the water molecules are immediately less likely to
diffuse (they are less mobile). So the effect of dissolving solute in water is to lower its
water potential. Consequently solutions at atmospheric pressure must have a negative
value of water potential (since pure water is set at zero). Also, the stronger the solution
(i.e. the more solute dissolved per volume of water) the larger the number of water
molecules that are slowed up and held almost stationary. So, in a very concentrated
solution, very many more of the water molecules have restricted movements than do
in a dilute solution.
EXTENSION
Solute potential
The amount of dissolved solute present in a solution is known as the solute potential
of the solution. It is given the symbol ψs. A simple osmometer is shown in Figure 4.13.
We use an osmometer to demonstrate the solute potential of a solution. Once the
osmometer is lowered into the beaker of water, very many more water molecules
diffuse across the membrane into the solution than move in the opposite direction.
The solution is diluted and it rises up the attached tube. An osmometer like this could
be used to compare the solute potentials of solutions with different concentrations.
This experiment can be

level of solution rises
carried out in your laboratory.
sucrose solution
(sucrose is the solute)
pure water
(water is the solvent)
partially permeable
membrane, e.g.
dialysis membrane
net inflow of water by osmosis, owing to

solute potential of the sucrose solution
▲ Figure 4.13 An osmometer
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EXTENSION
4
Pressure potential
Another The other factor that may influence osmosis is mechanical pressure acting on the solution. This factor is
given the name pressure potential. It is represented by the symbol ψp.
If a pressure greater than atmospheric pressure is applied to a solution, then this is an example of a pressure
potential being created in a solution. In the demonstration in Figure 4.14 a short length of dialysis tubing has been
set up to show how the pressure potential of a solution can become large enough to stop the osmotic uptake of

water altogether.
This experiment can be dialysis tubing bag now stretched by high internal pressure
carried out in your laboratory. (hydrostatic pressure) due to water uptake, i.e. it is in
a turgid condition
dialysis tubing
net water uptake ceases,
bag containing sucrose uptake of water owing to the hydrostatic pressure
solution is lowered by osmosis over time exerted by the dialysis bag, which
into water; bag shows
cannot be stretched any more
no signs of internal
pressure, i.e. it is in a
flaccid condition the pressure potential (yp)
has offset the solute potential (ys)
▲ Figure 4.14 Pressure potential at work
Questions 9 When a concentrated solution of sucrose is separated from a dilute solution of

sucrose by a partially permeable membrane, which solution:
a has a higher concentration of water molecules
b has lower water potential
c will experience a net gain of water molecules?
10 When a concentrated solution of glucose is separated from a dilute solution of
glucose by a partially permeable membrane, which solution:
a has a higher water potential
b has a higher concentration of water molecules
c will show a net gain of water molecules?
Osmosis in cells and organisms

Since water makes up 70–90 per cent of living cells and cell surface membranes are
partially permeable membranes, osmosis is very important in living things. We can
illustrate this first in plant cells.
Osmosis in plants
We need to think about the effects of osmosis in an individual plant cell first
(Figure 4.15, overleaf). There are two factors to consider.
» In a plant cell there is a cellulose cell wall. This is not present in an animal cell.
» In any cell the net direction of water movement depends upon whether the water
potential of the cell solution is more or less negative than the water potential of the
external solution.
When the external solution is less negative (that is, there is little or no dissolved
solutes), there is a net flow of water into the cell. The cell solution becomes diluted. The
volume of the cell is expanded by water uptake. As a result, the cytoplasm may come
to press hard against the cell wall. If this happens the cell is described as turgid and
further net uptake of water stops. Incidentally, the cell wall has actually protected the
delicate cell contents from damage due to osmosis.
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When the external solution is more negative (that is, much dissolved solutes), there is
a net flow of water out of the cell. The cell solution becomes more concentrated. As the
4 volume of cell solution decreases, the cytoplasm starts to pull away from parts of the
cell wall (contact with the cell wall is maintained at points where there are cytoplasmic
connections between cells). The cells are said to be plasmolysed (lysis means splitting)
and are flaccid.
when the external water potential is less when the external water potential is the when the external water potential is more
negative than the water potential of the cell same as the water potential of the cell negative than the water potential of the cell
net inflow no net water net outflow
of water cell is surrounded movement of water

cell solution by similar cells
diluted
cytoplasm cell solution
becomes more
concentrated
plasma membrane cellulose cell wall

(partially permeable) (fully permeable)
cell wall stretched and the cytoplasm pulls away from the cell wall;
cell is said to be turgid the cell is said to be plasmolysed and is
(prevents rupture of the cell surface membrane) flaccid
the external solution is less the external solution is the same the external solution is more
concentrated than the cell concentration as the cell solution concentrated than the cell
solution (a hypotonic solution) (an isotonic solution) solution (a hypertonic solution)
▲ Figure 4.15 A plant cell in changing external solutions
Estimation of the water potential of plant tissue

The net direction of water movement in a cell depends on whether the water potential
(ψ) of the cell solution is more negative or less negative than the water potential of the
external solution. We exploit this in our measurement of the water potential of plant
tissues. Representative samples of tissue are bathed in solutions of a range of water
potentials so that the solution which causes no net movement of water can be found.
This technique may be applied to plant tissue from which you can cut reproducible-
sized cylinders that will fit into a test tube or boiling tube. The tissue should be fully
turgid at the outset; soak in water to ensure this. Examples of suitable tissues would
include beetroot, potato tuber and carrot root. Cut the cylinders with a cork borer, wash
them in tap water, and finally measure their length (or cut them all to a standard length)
(Figure 4.16).
cylinders of tissue
cut with a cork
borer cylinders cut to a
standardised length
washed and soaked in

water to ensure turgidity
immersed in a sugar solution
of concentration of range
0.2 mol dm–3 (tube 1) to
1.0 mol dm–3 (tube 6)
1 2 3 4 5 6
finally, lengths of individual
cylinders are re-measured,
and change in length expressed
as a % of the original length
▲ Figure 4.16 Measuring water potential of plant tissue
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Steps to the experiment:
» Immerse (at least) one cylinder in each of the range of five sucrose solutions,
Sucrose
Water
potential 0.2 mol dm–3 to 1.0 mol dm–3 in a tube. Leave them immersed for one day. Set up a 4
(mol dm–3) (kPa) table to record the lengths of the tissue cylinders from each of the five tubes.
» Re-measure the length of each cylinder and record this in your table. Calculate the
0.2 –540 change in length as a percentage of the original length.
0.4 –1120 » Plot a graph of the percentage change in length against the molarity of the sucrose
0.6 –1800 solution. Read off the molarity of sucrose that causes no change in length of the tissue.
0.8 –2580 » Using the conversion table below, quote the water potential of the tissue you have

investigated.
1.0 –3510
▲ Table 4.2 The water In evaluating the experiment, consider the significant potential causes of error or
potential of sucrose inaccuracy in the technique. What improvements could you make?
solutions
Movement of water between plant cells
We have seen that water flows from a less negative to a more negative water potential.
When we discuss water movement through plants (Topic 7, page 149) we will see the
flow of water from cell to cell in roots. From root hair cells, where water uptake occurs
from a soil solution (of high water potential, i.e. less negative ψ), to the cells at the centre
of the root (of lower water potential, i.e. more negative ψ).
Plasmolysis in plant cells

Plasmolysis is most easily observed in cells with a coloured vacuolar solution. Examples
include beetroot tissue or the epidermis of rhubarb leaf stalks. There may be others local
to you (Figure 4.17).
Plasmolysed plant cells When they are placed in a solution of

In cells in which the solution in the water potential greater than that of the
vacuoles is coloured, they can be seen cell solution, plasmolysis of the cells
under the microscope whithout staining. can be observed by microscopy.
An external solution that

causes plasmolysis in 50 per cent
of the cells (incipient plasmolysis)
has the same water potential
as that of the cells.
▲ Figure 4.17 Plasmolysed plant cells
In the plasmolysed cell, the wall exerts no pressure at all. As a plasmolysed cell starts to
take up water the contents enlarge (Figure 4.18, overleaf). Water uptake stops when the
cells water potential reaches zero.
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plasmolysed
cell
4 water uptake
(dilution of cell solution)
fully turgid cell

cell contents
start to press
against the cell wall
–100
water potential/kPa
–200
–300
–400
–500 water potential
–600
–700
low increasing cell volume high
▲ Figure 4.18 Changing water potential of a plant cell
Plasmolysis and wilting

Typically, the cytoplasm of plant cells is undamaged by a period of plasmolysis. Cells
promptly recover when water becomes available. In non-woody plants (they are called
herbaceous plants, to tell them apart from trees and shrubs) a state of turgor is the
normal condition. The turgidity of all the cells plays a key part in the support of the plant
body. If herbaceous plants become short of water for a prolonged period, the plant wilts
(Figure 4.19). Ultimately, a wilted plant will die if it does not receive water.
well-watered potted plant with water loss continues; many cells of the leaves and stem
turgid cells become plasmolysed; flaccid cells provide no support
▲ Figure 4.19 Wilting
Osmosis in animals
An animal cell lacks the protection of a cellulose cell wall. Consequently, compared
with a plant cell, it is very easily damaged by changes in the external solution. If a
typical animal cell is placed in pure water, the cell surface membrane will break apart
quite quickly.
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when the external water when the external water when the external water
potential is less negative potential is the same as the potential is more negative
than the water potential
of the cell
water potential of the cell,
e.g. in the blood plasma
than the water potential of
the cell 4
no net water
movement net outflow
of water
cell bursts cell outline
becomes
crinkled

cell solution becomes
more concentrated
net inflow
of water
▲ Figure 4.20 A red blood cell in changing external solutions
Figure 4.20 shows what happens to an animal cell (a red blood cell) when the external
solution has a water potential that is both less negative and more negative than the cell
solution.
In most animals (certainly in mammals) these problems are avoided because the osmotic
concentration of body fluids – the blood plasma and tissue fluid – is very precisely
regulated. The water potential is regulated both inside and outside body cells (to
maintain isotonic conditions). This process is known as osmoregulation (Topic 14).
Aquatic, unicellular animals

Many unicellular animals live in aquatic environments and survive even though their
surroundings have a water potential substantially less negative than the cell solution.
All the time, water is flowing into these cells by osmosis. They are in constant danger
that their membrane will burst because of high internal pressure. In fact the problem is
overcome – or rather, prevented.
The protozoan Amoeba (Figure 4.21) is one example. The cytoplasm of an amoeba
contains a tiny water pump, known as a contractile vacuole. This works continuously
to pump out the excess water. How important the contractile vacuole is to the organism
is fatally demonstrated if the cytoplasm is temporarily anaesthetised – the Amoeba
quickly bursts.
nucleus
Question
pond water –
11 What is the outcome water potential cytoplasm
of immersing less negative than
an animal cell water potential of
cytoplasm solution
in a solution of
of Amoeba
substantially lower
contractile vacuole:
water potential than water collects here
that of the cell? What net inflow of water and is then expelled
would be the effect over the whole from the cell by the
on a plant cell? cell surface membrane pumping action of
the vacuole
▲ Figure 4.21 The role of the contractile vacuole in Amoeba
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Polar water molecules and the lipid bilayer – a recap
4 We have seen that water enters and leaves cells by osmosis, yet the lipid bilayer of the
cell surface membrane is at least theoretically impermeable to polar water molecules.
However, water molecules are very small and it is likely that there are many tiny
spaces open between the giant molecules of the lipid bilayer. Remember, the lipid
molecules are also constantly moving about. In addition, quite small, protein-lined
pores exist in the membrane and are permanently open (Figure 4.22). These proteins
allow unrestricted water movement because the pore is lined by hydrophilic amino
acid residues.
small,
protein-lined
pores provide
molecules of the
permanent
lipid bilayer are
channels for
always on the
diffusion of
move, producing
water
tiny (short-lived)
molecules
pores that are
large enough for
water molecules
to pass through
▲ Figure 4.22 How polar water molecules cross the lipid bilayer
Movement by active transport

Active transport is the selective movement of molecules across a membrane. In active
transport, metabolic energy produced by the cell and held as ATP is used to drive
the transport of molecules and ions across membranes against the concentration
gradient. Active transport has characteristic features distinctly different from those of
movement by diffusion. These are as follows.
1 Active transport may occur against a concentration gradient

Molecules can be moved by active transport from a region of low concentration to a
region of higher concentration. The cytosol of a cell normally holds some reserves
of molecules valuable in metabolism, like nitrate ions in plant cells or calcium
ions in muscle fibres. The reserves of useful molecules and ions do not escape; the
cell surface membrane retains them inside the cell. However, when more useful
molecules or ions become available for uptake, they are actively absorbed into the
cells. This uptake occurs even though the concentration outside is lower than the
concentration inside.
2 Active uptake is a highly selective process

For example, in a situation where potassium chloride, consisting of potassium (K +)
and chloride (Cl−) ions, is available to an animal cell, it is the potassium ions that are
more likely to be absorbed, since they are needed by the cell. Where sodium nitrate,
consisting of sodium (Na+) and nitrate (NO3 −) ions, is available to a plant cell, it is
likely that more of the nitrate ions are absorbed than the sodium ions, since this too
reflects the needs of these cells.
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3 A
ctive transport involves special molecules of the membrane called
‘pumps’
The pump protein picks up particular molecules and transports them to the other 4
side of the membrane, against the the concentration gradient, where they are
then released. Pump proteins are globular proteins that traverse the lipid bilayer.
Movements by these pump proteins require energy from ATP. By means of this
reaction, metabolic energy is supplied to the process. Most membrane pumps are
specific to particular molecules. This is the way selective transport is brought about. If
the pump protein for a particular substance is not present, the substance will not be

transported.
Active transport is a feature of most living cells. We meet examples of active transport
in the gut where absorption occurs, in the active uptake of ions by plant roots, in
the kidney tubules where urine is formed, and in nerves fibres where an impulse is
propagated. We discuss some of these examples later.
1 2
carrier
molecules protein P
to be AT
in lipid
transported bilayer
into cell
carrier protein
activated by
reaction
with ATP
ADP and Pi released

from carrier protein,
4 which reverts to the 3
receptive shape
change in
shape and
molecule
position of
released
carrier
protein ADP
+P
i
▲ Figure 4.23 Active transport of a single substance
The protein pumps of cell surface membranes are of different types. Some transport a
particular molecule or ion in one direction (Figure 4.23). Occasionally, two substances
are transported in the same direction; for example, Na+ and glucose. Others transport
two substances (like Na+ and K+) in opposite directions (Figure 4.24, overleaf).
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A case study: the structure and function of sodium–potassium
pumps in axons
4 A nerve impulse is transmitted along the axon of a nerve cell by a momentary reversal in
electrical potential difference in the axon membrane, brought about by rapid movements
of sodium and potassium ions. You can see the structure of a nerve cell and its axon in
Figure 15.3, page 320.
Sodium–potassium pumps are globular proteins that span the axon membrane. In
the preparation of the axon for the passage of the next nerve impulse, there is active
transport of potassium (K+) ions in across the membrane and sodium (Na+) ions out
across the membrane. This activity of the Na+ –K+ pump involves transfer of energy from
ATP. The outcome is that potassium and sodium ions gradually concentrate on opposite
sides of the membrane. The steps to the cyclic action of these pumps are:
1 With the interior surface of the pump open to the interior of the axon, three sodium
ions are loaded by attaching to specific binding sites.
2 The reaction of the globular protein with ATP now occurs, resulting in the
attachment of a phosphate group to the pump protein. This triggers the pump
protein to close to the interior of the axon and open to the exterior.
3 The three sodium ions are now released, and simultaneously, two potassium ions are
loaded by attaching to specific binding sites.
4 With the potassium ions loaded, the phosphate group detaches. This triggers a
reversal of the shape of the pump protein; it now opens to the interior, again, and the
potassium ions are released.
5 The cycle is now repeated again.
2 changes in shape 3
and position of
K+ ions loaded
1 carrier protein
carrier protein ADP
Pi Pi
ATP
activated by
reaction with ATP
Na+ ion
Na+ ions released
carrier protein
in lipid bilayer K+ ions loaded
▲ Figure 4.24 The sodium–potassium ion pump
Question 12 Samples of five plant tissue disks were incubated in dilute sodium chloride solution
at different temperatures. After 24 hours it was found that the uptake of ions from
the solutions were (in arbitrary units):
Sodium ions Chloride ions
Tissue at 5°C 80 40
Tissue at 25°C 160 80
Comment on how absorption of sodium chloride occurs, giving your reasons.
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Movement by bulk transport
Bulk transport occurs by movements of vesicles of matter (solids or liquids) across the
cell surface membrane. The flexibility of the fluid mosaic membrane makes this activity 4
possible, and energy from metabolism (ATP) is required. Figure 4.25 shows this form of
transport across a cell surface membrane.

nucleus
uptake of solid particles = phagocytosis cytoplasm
uptake of matter = endocytosis
uptake of liquid = pinocytosis
▲ Figure 4.25 Movement by bulk transport
Exocytosis is the process by which cells export products such as enzymes by means
of vesicles. We have seen that vesicles may be budded off from the Golgi apparatus
(Figure 1.15, page 17). The vesicles are then guided to the cell surface membrane by the
network of microtubules in the cytosol. Here they fuse with the membrane and their
contents are discharged to the outside of the cell.
Alternatively, waste matter may be disposed of at the cell surface, in a similar way.
By the reverse process, endocytosis, substances may be imported into the cell. Here,
fresh vesicles are formed at the cell surface. This occurs when part of the cell surface
membrane forms a ‘cup’ around a particle or a drop of fluid, and encloses it to form a
vesicle. This vesicle is then brought into the cytosol.
The wholesale import of solid matter in this way is termed phagocytosis. In the human
body, there is a huge force of phagocytic cells, called the macrophages. Some of these
mop up debris of damaged or dying cells and break it down. For example, we dispose
of about 3 3 1011 red blood cells each day. All of these are ingested and disposed of by
macrophages.
Pinocytosis is bulk import of fluids and occurs in the same way. Bulk uptake of lipids
by cells lining the gut occurs as part of the digestion process, for example.
Questions 13 Phagocytic cells are also found in the airways of the lungs. What is their role and
how do they carry it out?
14 Distinguish between the following pairs.
a proteins and lipids in cell membranes
b active transport and bulk transport
c hypotonic and hypertonic solutions
d endocytosis and exocytosis
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A summary of the functions of membrane proteins
4 We can now see that the proteins of the cell surface membrane, scattered about and
across the lipid bilayer as they are, show diversity in function – all highly significant in
the life of a cell. These functions are summarised in Figure 4.26.
channel protein for

1 channels for transport
passage through
of metabolites or water
membrane – each channel
allows one specific
substance to pass
pump protein for

active transport
across membrane –
energy from ATP
is used selectively to
move one (or two)
ADP + Pi
specific substances
ATP
across
electron carrier proteins –

2 enzymes and carriers a chain of peripheral and e–
integral proteins that allow
electrons to pass across the
membrane (Topic 12)
e–
enzymes held in membrane –
catalyse reactions at surface of
membrane, within or outside
the cell
active site – the

substrate molecule
fits here and the
reaction then occurs
binding protein for

3 receptors, antigens, attachment of a specific
cell–cell recognition hormone – a signal is then
and cell binding sites generated that is transmitted
inside the cell (Topic 14)
cell–cell recognition site –

attachment may result in
cells binding together
binding sites
for antigen–antibody reaction
(Topic 11)
▲ Figure 4.26 The functions of membrane proteins – a summary
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SUMMARY
» The cell surface membrane is an organelle that » The name given to the tendency of water
4
surrounds and contains the cell contents. Across it molecules to move about is water potential. The
there is a continuous movement of the molecules Greek letter psi (symbol y) is used to represent
needed by cells or being disposed of by them. water potential. Water moves from a region of
» The membrane consists of lipids and proteins with higher water potential to a region of lower water
a small amount of carbohydrate. The lipids are potential – down a water potential gradient .
phospholipids, molecules with a hydrophilic head Equilibrium is reached only if or when the water

and a hydrophobic tail, organised into a bilayer potential is the same in both regions. At this point,
with the heads on the outsides. The proteins are there would be no net movement of water from
globular proteins arranged in, across and on the one region to another, but random movements of
surface of the lipid bilayer. Short carbohydrate water molecules continue.
chains are attached to some of the proteins » Solute molecules in solution are surrounded by
and lipids on the outside. In addition, a variable water molecules held by hydrogen bonds. In a
quantity of molecules of cholesterol occurs, concentrated solution, few water molecules are
inserted between some of the lipid molecules. free to move. Therefore there is net diffusion
» The membrane is described as a fluid mosaic , of free water molecules in pure water or a
as the components (particularly the lipids) move dilute solution (free water molecules in high
about laterally, relative to each other, and the concentration), through a partially permeable
proteins appear to be randomly scattered about. membrane (such as the cell surface membrane),
The cholesterol regulates membrane fluidity. into a more concentrated solution (where free
» There are three mechanisms of transport across water molecules are in low concentration) – a
membranes. In diffusion (and osmosis, a special process known as osmosis.
case of diffusion) the energy comes from the » Active uptake is a selective process and involves
kinetic energy of matter. In active transport (i.e. the accumulation of ions and organic substances
pumping) and in bulk transport , the energy is against a concentration gradient . The process is
provided indirectly from cell metabolism, via ATP. powered by metabolic energy and involves highly
» Diffusion occurs from a region of high specific protein molecules in the membrane that act
concentration to a region of low concentration. as pumps.
The lipid bilayer of the cell surface membrane » Bulk transport is the movement of the contents
acts as a barrier, at least to polar substances. of vesicles (tiny, membrane-bound sacs) of
Polar substances such as water diffuse through matter, solid or liquid, into (endocytosis) or out of
tiny pores or small spaces in the bilayer. Some (exocytosis) the cell.
molecules react with a membrane protein to open
a specific channel (facilitated diffusion).
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4 1 Fig. 1.1 is a diagram of a cell surface membrane.
▲ Fig. 1.1
a Use a label line and the appropriate letter to label each of the following on a
copy of Fig. 1.1.
P protein for active uptake of potassium ions
Q protein for facilitated diffusion of polar molecules
R receptor site for a hormone
S hydrophilic heads of phospholipids on the internal surface of the membrane
T molecule that modifies the fluidity of the membrane [5]
b Some cells take in bacteria by endocytosis.
Explain how endocytosis occurs at a cell surface membrane. [3]
[Total: 8]
(Cambridge International AS and A Level Biology 9700 Paper 21 Q1 Oct/Nov 2011)
2 The cell surface membrane has a fluid mosaic structure.
a Describe what is meant by the term fluid mosaic. [2]
protein
phospholipid
bilayer
protein
▲ Fig. 2.1
b In 1934, the biologists Davson and Danielli published their suggestion for the
structure of the cell surface membrane, as shown in Fig. 2.1.
They suggested that the membrane was a phospholipid bilayer with a layer of
hydrophilic protein on both surfaces.
State one way in which the Davson-Danielli structure is similar to the
fluid mosaic structure and one way in which it differs from the fluid
mosaic model. [2]
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c One way in which substances can cross cell membranes is by
active transport.
Describe the mechanism of active transport. [3] 4
d High temperature can damage cell membranes. One factor contributing to
this damage is the denaturation of membrane proteins.
Describe how proteins become denatured at high temperature and explain how
this could lead to damaging cell membranes. [3]
[Total: 10]

3 Thirty strips of plant tissue of measured, standard length were cut, quickly
washed, and then blotted dry. To each of three small beakers were added 10
strips and the tissue samples were immersed in sucrose solution of different
concentrations. After a period of 30 minutes, the tissue strips were removed and
their length remeasured. The results were as follows:
Beaker 1 2 3
Sucrose solution (mol dm3) 0.1 0.4 0.8
Change in length of tissue strips increase no change decrease
a Why were the tissue strips briefly washed and blotted dry before
measurement? [1]
b Why did the experimenter use a sample of 10 strips in each treatment? [2]
c Explain what events in the cells of the tissue strips in beaker 1 during the
experiment bring about their change in length. [6]
d Explain what events in the cells of the tissue strips in beaker 3 during the
experiment bring about their change in length. [6]
e What can you conclude from the results from the tissue sample in
beaker 2? [3]
f For what reason is osmosis described as a special case of diffusion? [2]
[Total: 20]
4 Design and outline a laboratory experiment to investigate the effect of
temperature on the cell surface membrane.
Use samples of plant tissue that contains an intensely
red, water-soluble pigment in the cell vacuoles (such as beetroot).
a What steps would you take to ensure the significance of your results?
b What outcomes to your experiment do you expect?
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AS LEVEL

When body cells reach a Learning outcomes

certain size they divide into
two cells. Nuclear division
occurs first, followed by 5.1.1 describe the structure of a chromosome, limited to: DNA, histone
division of the cytoplasm. proteins, sister chromatids, centromere and telomeres
The mitotic cell cycle of 5.1.2 explain the importance of mitosis in the production of genetically identical
eukaryotes involves DNA daughter cells during: growth of multicellular organisms, replacement of
replication followed by damaged or dead cells, repair of tissues by cell replacement and asexual
nuclear division. This ensures reproduction
the genetic uniformity of all
daughter cells.
5.1.3 outline the mitotic cell cycle, including: interphase (growth in G1 and G2
phases and DNA replication in S phase), mitosis and cytokinesis
5.1.4 outline the role of telomeres in preventing the loss of genes from the ends
of chromosomes during DNA replication
5.1.5 outline the role of stem cells in cell replacement and tissue repair by
mitosis
5.1.6 explain how uncontrolled cell division can result in the formation of a
tumour
Starting points
★ During the mitotic cell cycle, DNA is replicated and passed to daughter cells.
★ Stem cells in bone marrow and the skin continually divide by mitosis to
provide a continuous supply of cells that differentiate into blood and skin
cells.
5.1 Replication and division of nuclei and cells

The division of cells
New cells arise by division of existing cells. In this process, the first step is for the
nucleus to divide. The cytoplasm then divides around the daughter nuclei.
Unicellular organisms grow quickly under favourable conditions. They then divide
in two. This cycle of growth and division is repeated rapidly, at least while conditions
remain supportive.
In multicellular organisms the life cycle of individual cells is more complex. Here, life
begins as a single cell which grows and divides, forming many cells. These eventually
make up the adult organism. Certain of these cells retain the ability to grow and divide
throughout life. They are able to replace old or damaged cells. However, the majority of
the cells of multicellular organisms become specialised. Most are then unable to divide
further.
The importance and role of the nucleus

The structure of the nucleus was introduced in Topic 1 (page 15). The nucleus is the
organising centre of a cell, and has a double function. Firstly, it controls all the activities
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of the cell throughout life. Secondly, it is the location within the cell of the hereditary
material, which is passed from generation to generation during reproduction. Both of the
functions depend on ‘information’. The information in the nucleus is contained within
structures called chromosomes. These uniquely:
5
» control cell activities
» are copied from cell to cell when cells divide
» are passed into new individuals when sex cells fuse together in sexual reproduction.
So, the nucleus contains the chromosomes of the cell, and the chromosomes contain

the coded instructions for the organisation and activities of cells and for the whole
organism. It is on the structure of the chromosomes that we focus first.
Introducing chromosomes
At the time a nucleus divides the chromosomes become compact, much-coiled structures.
Only in this condensed state do the chromosomes become clearly visible in cells,
provided they have been treated with certain dyes, At all other times, the chromosomes
are very long, thin, uncoiled threads. In this condition they give the stained nucleus a
granular appearance. The granules are called chromatin.
The information the nucleus holds on its chromosomes exists as a nucleic acid called
deoxyribonucleic acid (DNA). DNA is a huge molecule made up of two paired strands
in the form of a double helix (Figure 6.4, page 123). A single, enormously long DNA
molecule runs the full length of each chromosome.
Look up the structure of DNA now.
The chromosomes are effectively a linear series of genes. A gene is a sequence of nucleotides
that forms part of a DNA molecule. It codes for a single polypeptide and is capable of
determining the development of a specific characteristic of an organism. A particular gene
always occurs on the same chromosome in the same position.
There are four features of the chromosomes that are helpful to note at the outset:
» The shape of a chromosome is characteristic. Chromosomes are long, thin
structures of a particular, fixed length. Somewhere along the length of the
chromosome occurs a short, constricted region called the centromere. A centromere
may occur anywhere along the chromosome, but it is always in the same position
on any given chromosome. The position of the centromere, as well as the length of a
chromosome is how they are identified in photomicrographs.
» The number of chromosomes per species is fixed. The number of chromosomes
in the cells of different species varies, but in any one species the number of
chromosomes per cell is normally constant. For example, the mouse has 40
chromosomes per cell, the onion has 16, humans have 46, and the sunflower 34.
These are the chromosome numbers for the species. Please note that these are all
even numbers.
» Chromosomes occur in pairs. The chromosomes of a cell occur in pairs, called
homologous pairs (meaning ‘similar in structure’). One of each pair came originally
from each parent. So, for example, the human has 46 chromosomes, 23 coming
originally from each parent in the process of sexual reproduction. This is why
chromosomes occur in homologous pairs.
» Chromosomes are copied. Between nuclear divisions, while the chromosomes are
uncoiled and cannot be seen, each chromosome is copied. This copying process
occurs in the cell before nuclear division occurs. The two identical structures
formed are called sister chromatids. The chromatids remain attached by their
centromeres until they are divided during nuclear division. Then the centromeres
and the chromatids separate. After this separation, the chromatids are recognised
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as chromosomes again. Of course, when chromosomes copy themselves the
critical event is the copying of the DNA double helix that runs the length of the
5 chromosome. This is known as replication of the DNA. You will discover how this
replication process is brought about in Topic 6.
The changing appearance of a chromosome
in the nucleus, not after the chromosome has as a consequence of nuclear

yet duplicated made a copy of itself division (mitosis)
centromere *
Question
1 Explain why
chromosomes occur
in homologous pairs
in cells.
The chromosome will be Well before mitosis (nuclear division) During mitosis the two
an extended DNA molecule occurs the chromosome duplicates. chromatids separate and
with associated protein – rather The two copies are still attached at are distributed to the
than as shown here in the centromeres and are known as daughter nuclei that
condensed form. sister chromatids. are formed.
▲ Figure 5.1 One chromosome as two chromatids
The structure of chromosomes

We have already noted that each chromosome consists of a macromolecule of DNA
in the form of a double helix. This runs the full length of the chromosome. However,
it is supported by protein. About 50 per cent of a chromosome is built of protein.
Some of these proteins are enzymes that are involved in copying and repair reactions
of DNA. However, the bulk of chromosome protein has a support and packaging role
for DNA.
Why is packaging necessary?
Well, take the case of human DNA. In each nucleus, the total length of the DNA of the
chromosomes is over 2 metres. We know this is shared out between 46 chromosomes.
Chromosomes are of different lengths, but we can estimate that within a typical
chromosome of 5 μm length, there is a DNA molecule approximately 5 cm long. This
means that about 50 000 μm of DNA is packed into 5 μm of chromosome.
This phenomenal packaging problem is achieved by the much-coiled DNA double
helix being looped around protein beads consisting of a packaging protein called
histone (Figure 5.2). This is a basic (positively charged) protein containing a high
concentration of amino acid residues with additional base groups (–NH 2 ), such
as lysine and arginine. Eight histone molecules combine to make a single bead.
Around each bead, the acidic (negatively charged) DNA double helix is wrapped in
a double loop.
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drawing of the chromosome showing the packaging of DNA
5
Here the structure is progressively unpacked chromatids
to show how a huge molecule of DNA is held
and supported, by:
1) double-coiling around histone proteins
(bead structures = nucleosomes) and then
2) looped along the length of the chromatid,
electron micrograph of chromosome attached to a protein scaffold.
during mitosis (metaphase) – showing

two chromatids held together at the
centromere
centromere (×40 000)
(in the interphase

nucleus the DNA
is dispersed as a
looped strand,
suspended around
the scaffold protein)
scaffold protein
(not histone)
(typically a DNA molecule loops of the

of about 5 cm in length is cylindrical
packed into each chromatid of coiled fibre cylindrical coil
approximately 5 μm in length) of the chromatin
fibre
30 nm
H1 histone binds
the DNA to the
to next histone ‘bead’
nucleosome
DNA double helix

DNA double helix
wound round histone
wound twice around
protein ‘bead’ – called
histone core
a nucleosome
2 nm DNA double helix
Also present are enzymes

involved in the transcription
and replication of the DNA.
core of nucleosome
of eight histone
molecules – forming
a ‘bead’ structure
▲ Figure 5.2 The packaging of DNA in the chromosome – the role of histone protein
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Question At times of nuclear division the whole beaded thread is itself coiled up, forming the
chromatin fibre. The chromatin fibre is again coiled, and the coils are looped around a
5 2 Deduce the
significance of the
‘scaffold’ protein fibre, made of a non-histone protein. This whole structure is folded
(supercoiled) into the much-condensed chromosome. This arrangement enables the safe
positively charged storage of these phenomenal lengths of DNA that are packed in the nuclei. However, it also
histone protein allows access to selected lengths of the DNA (particular genes) during transcription – a
and the negatively process you will encounter in Topic 6.
charged DNA.
This is the arrangement in the nuclei of eukaryotes. We can conclude that the single
circular chromosome of prokaryotes does not present the same packaging problem, for
in these organisms the DNA is described as ‘naked’. It occurs without the support of any
protein.
The nature and significance of telomeres

genes Each time the DNA of the chromosomes is copied (replicated), prior
to mitosis and cell division, the ends of the DNA molecules cannot
be copied. As a result, a few terminal nucleotide sequences are lost.
With repeated replications comes progressive shortening on the
DNA of each chromosome. If the ends were not protected in some
way, chromosomes would lose genes or parts of genes. In fact the
ends are protected by special, non-coding nucleotide sequences
region of called telomeres. Typically, a telomere consists of a six-nucleotide
telomeres
sequence such as ‘TTAGGG’, repeated up to a thousand times. It is
parts of this non-coding sequence that are lost at each replication of
the DNA, without any harm to the genes the chromosome carries.
The chromosomes in nuclear division

Divisions of the nucleus are very precise processes, ensuring the
correct distribution of chromosomes between the daughter cells.
There are two types of nuclear division, known as mitosis and
▲ Figure 5.3 The position of telomeres
meiosis.
In mitosis, the genetically identical daughter cells produced have the same number of
chromosomes as the parent cell, typically two of each type and this is known as the
diploid (2n) state. Mitosis is the nuclear division that occurs when: cells grow or when
cells need to be replaced and when an organism reproduces asexually.
In meiosis, the daughter cells contain half the number of chromosomes of the parent
cell. That is, one chromosome of each type is present in the nuclei formed and this is
known as the haploid (n) state. Meiosis is the nuclear division that occurs when sexual
reproduction occurs, typically during the formation of the sex cells (called gametes) (see
pages 345–8).
Whichever division takes place, it is normally followed by division of the cytoplasm to
form separate cells. This process is called cytokinesis.
The significance of mitosis

Each daughter cell produced by mitosis has a full set of chromosomes, identical to those
of the parent cell. No variation in genetic information arises by mitosis.
Question In the growth of a multicellular organism it is essential that all cells carry the same
genetic information (the same chromosomes) as the existing cells of the organism.
3 What are the
Similarly, when repair of damaged tissues or worn out cells occurs, the new cells must
essential differences
be exact copies of the cells being replaced. Mitosis ensures this. Otherwise, in growth,
between mitosis and
development and repair activities, different parts of the body of an organism might start
meiosis?
working to conflicting blueprints. The results would be chaos.
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cell about to divide
nuclear 5
envelope
first the chromosomes
nucleolus appear as thin threads
chromatin

mitosis meiosis
nuclear division by mitosis occurs when nuclear division by meiosis occurs when sexual
organisms grow and develop, and tissues reproduction occurs (e.g. when gametes are
are repaired or replaced formed in mammals and plants)
Two cells formed, each containing two sets of

chromosomes (two copies of each homologous
chromosome) – diploid (2n).
Question
4 a What is a haploid
cell?
b Where in the
human body
would you find Four cells formed, each containing only
cells undergoing: one set of chromosomes (only one of
each homologeous chromosome) –
i meiosis haploid (n).
ii mitosis?
▲ Figure 5.4 Mitosis and meiosis: the significant differences
In asexual reproduction, of which various forms exist, the offspring produced are
identical to the parent since they are produced as a result of mitotic cell division. As a
consequence, the offspring have all the advantages of the parents in mastering the same
habitat – and any disadvantages, too. The offspring produced by asexual reproduction
are often described as clones.
Mitosis and the cell cycle

The cell cycle is the sequence of events that occur between one division and the next
(Figure 5.5). It consists of three main stages: interphase, nuclear division (mitosis) and
finally cell division (also called cytokinesis). The length of the cycle depends partly
upon conditions external to the cell, such as temperature, supply of nutrients and oxygen.
Its length also depends upon the type of cell. In cells at the growing point of a young
stem or of a developing human embryo, the cycle is completed in less than 24 hours. The
epithelium cells that line the gut typically divide every 10 hours. Liver cells divide every
year or so. Nerve cells never divide again, after they have differentiated. Here the nucleus
remains at interphase. In specialised cells the genes, other than those needed for the
specific function, are ‘switched off’, so they cannot divide.
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the cell cycle Key change in cell volume and quantity of DNA during a cell cycle
quantity mitosis and
5 G2 = interphase
cell growth of DNA cell division
continues
prophase replication of
mitosis
metaphase chromosomes
anaphase M
telophase
cell cycle cell division
(cytokinesis):
two cells
formed
volume
S of cell
chromosomes G1
are copied cell grows,
producing new
organelles
The DNA of the
chromosome is copied
(replicated)
length of cell cycle (time)
during interphase.
▲ Figure 5.5 The stages of the cell cycle
Interphase
Interphase is always the longest part of the cell cycle but it is of extremely variable
length. At first glance the nucleus appears to be ‘resting’ but this is not the case at all.
The chromosomes, previously visible as thread-like structures, have become dispersed.
Now they are actively involved in protein synthesis – at least for most of interphase.
From the chromosomes, copies of the information of particular genes or groups of genes
are taken in the form of ribonucleic acid (RNA) (‘messenger RNA’, page 136) for use
in the cytoplasm. In the cytoplasm, ribosomes assemble proteins from amino acids,
combining them in sequences dictated by the information from the gene. We return to
this process later in this topic.
Look at Figure 5.5. The sequence of the events of interphase is illustrated there. The
changes that occur are summarised in Table 5.1.
G1: the ‘first The cell grows by producing proteins and cell organelles, including
gap’ phase mitochondria and endoplasmic reticulum.
S: synthesis Growth of the cell continues as replication of DNA occurs (see Topic 6).
Protein molecules called histones are synthesised and attach to the
DNA.
Each chromosome becomes two chromatids.
G2: the ‘second Cell growth continues by protein and cell organelle synthesis.
gap’ phase Mitochondria and chloroplasts divide.
The spindle begins to form.
Nuclear division, mitosis (M), follows.
▲ Table 5.1 The events of interphase
Mitosis
Daughter cells produced by mitosis have a set of chromosomes identical to each other
and to the parent cell from which they were formed because:
» an exact copy of each chromosome is made by accurate copying during interphase,
when two chromatids are formed
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plant cell after nucleus has divided
cytoplasm ER secretes vesicles of

wall-forming enzymes
5
daughter nucleus
remains of the
spindle
Golgi apparatus daughter cells
secretes vesicles
of wall components

cell plate
(equator of vesicles collect at the midline
spindle)
then fuse to form cell wall
layers and new cell surface membrane
cellulose cell wall
▲ Figure 5.6 Cytokinesis in a plant cell
» chromatids remain attached by their centromeres during metaphase of mitosis,

when each becomes attached to a spindle fibre at the equator of the spindle
» centromeres then separate during anaphase and the chromatids of each pair are
pulled apart to opposite poles of the spindle. Thus, one copy of each chromosome
moves to the poles of the spindle
» the chromosomes at the poles form the new nuclei – two to a cell at this point
» two cells are then formed by separation of the cytoplasm at the mid-point of the cell,
each with an exact copy of the original nucleus.
Cytokinesis
Cytokinesis is the division of the cytoplasm that follows telophase. During cytokinesis,
cell organelles such as mitochondria and chloroplasts become evenly distributed
between the cells. In animal cells, the cytoplasm separates by in-tucking of the cell
surface membrane at the equator of the spindle, ‘pinching’ the cytoplasm in half
In plant cells, the Golgi apparatus forms vesicles of new cell wall materials which collect
along the line of the equator of the spindle, known as the cell plate. Here the vesicles
fuse, forming the new cell surface membranes and the cell walls between the two cells
(Figure 5.6).
The role of stem cells in cell replacement and tissue repair

Small groups of stem cells – cells that are capable of self-renewal and of producing new
cells that differentiate into other specialised types of cell – are found in the tissues of
adults, where their general function is to repair damaged cells or replace lost cells. These
cells are called adult stem cells. Unlike embryonic stem cells, which have the ability to
produce every one of the different cells identified in textbooks of human histology, adult
stem cells are either unipotent or, at best, multipotent.
» Unipotent cells can divide to replicate itself and to produce only one type of cell, for
example cells in the germinal epithelium of the skin.
» Multipotent cells can divide to replicate itself and to produce the different cells in
one type of tissue, for example haematopoietic cells in bone marrow that give rise to
red blood cells, white blood cells and platelets.
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Cancer – diseases of uncontrolled cell division
5 Today, in developed countries, one in three people suffer from cancer at some point in
their life and approximately one in four will die from it. In these regions the commonest
cancers are of the lung in males and of the breast in females. However, in many parts of
the world, cancer rates are different – often they are significantly lower. You can see the
range of common cancers and their incidences worldwide at: http://globocan.iarc.fr/
Cancer is the result of the ill-regulated proliferation of cells, typically resulting in the
formation of a solid tumour. There are many different forms of cancer, affecting different
tissues of the body – cancer is not thought of as a single disease. Cancers are usually
fatal if untreated. Today, many cancers are treatable, and in these cases, survival rates
are improving markedly.
So, cancer arises when the cell cycle operates without its normal controls. In a healthy cell
the cell cycle is regulated by a molecular control system, itself controlled by specific genes.
However, cells may start to divide by mitosis, repeatedly, without control or regulation.
Now the rate of cell multiplication is very much faster than the rate of cell death, and an
irregular mass of cells, a tumour, is formed (Figure 5.7).
Normally dividing cells subjected

to prolonged exposure to
carcinogens. The mutated cell undergoes repeated,
rapid mitosis (the cell cycle is not
ultraviolet light inhibited). The cells formed do not
tobacco smoke respond to signals from other cells and
are not removed by the immune system.
asbestos The carcinogen causes

mutation in a cell.
X-rays
mitosis
abnormal cells rapid

(do not cause serious mitosis
problems and can
be removed by surgery)
A benign tumour absorbs nutrients, enlarges,

may compress surrounding tissues, but
does not spread from its site of initiation.
rapid
Malignant tumour cells
mitosis
may have unusual
chromosomes and
This step is possible
their metabolism is
but not inevitable.
disabled.
lymph blood
vessel vessels
This step is possible A malignant tumour consists of cells that
but not inevitable. secrete signals triggering growth of blood and
lymph vessels to serve the tumour cells at the
expenses of other tissues. Attachments to
other cells are lost and then malignant cells
may be carried around the body setting up
secondary growths. The functions of invaded
organs are typically impaired or obstructed.
The spread of cancer cells to other locations

is called metastasis.
▲ Figure 5.7 Steps in the development of a malignant tumour
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Cancers start when changes occur in the genes that regulate the cell cycle. This is where
carcinogens may enter the story. A carcinogen is any agent that may cause cancer. Some
highly significant carcinogens are identified in Table 5.2. 5
So, carcinogens are highly likely to cause damage to the DNA molecules of
chromosomes. The result is a mutation – a change in the amount or chemical structure
of DNA of a chromosome. Mutations of different types build up in the DNA of body cells
over time. A single mutation is unlikely to be responsible for triggering cancer. With
time, mutations may accumulate in the body and then trigger a disease. This explains
why the majority of cancers arise in older people. Also, mutation may occur in the cells
5.2 Chromosome behaviour in mitosis

of different body tissues, and hence cancer is not one single disease.
Question Ionising Ionising radiation includes X-rays and radiation (gamma rays, α
radiation particles, β particles) from various radioactive sources. These may
5 Describe three trigger the formation of damaging ions inside the nucleus – leading to
environmental the break-up of the DNA.
conditions that may
cause normal cells Non-ionising Non-ionising radiations such a UV light. This is less penetrating than
to become cancerous radiation ionising radiation, but if it is absorbed by the nitrogenous bases of
cells. DNA, may modify it – causing adjacent bases on the DNA strand to
bind to each other, instead of binding to their partner on the opposite
strand (page 123).
Chemicals Several chemicals that are carcinogens are present in tobacco smoke.
Also, prolonged exposure to asbestos fibres may trigger cancer in the
linings of the thorax cavity – the harm usually becomes apparent only
many years later.
▲ Table 5.2 Common carcinogens known to increase mutation rates and the likelihood of
cancer

Learning outcomes
5.2.1 describe the behaviour of chromosomes in plant and animal cells
during the mitotic cell cycle and the associated behaviour of the nuclear
envelope, the cell surface membrane and the spindle (names of the main
stages of mitosis are expected: prophase, metaphase, anaphase and
telophase)
5.2.2 interpret photomicrographs, diagrams and microscope slides of cells in
different stages of the mitotic cell cycle and identify the main stages of
mitosis
Starting point
★ The events that occur during mitosis can be followed by using a light
microscope.
Behaviour of chromosomes during the mitotic cell cycle

In mitosis, the chromosomes, present as the chromatids formed during interphase, are
separated and accurately and precisely distributed to two daughter nuclei. Here, mitosis
is presented and explained as a process in four phases but this is for convenience of
description only. Mitosis is one continuous process with no breaks between the phases.
Follow the phases of mitosis in Figure 5.8.
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interphase
5
For simplicity, the drawings cytoplasm
show mitosis in a cell with nuclear
a single pair of homologous chromatin
envelope
chromosomes.
cell surface
centrosome consisting of
membrane
pair of centrioles
nucleolus
cytokinesis
Chromosomes are shown here as

divided into chromatids, but this

division is not immediately visible. centrioles
cytoplasm duplicate
divides
prophase
spindle chromosomes
disappears uncoil nucleolus chromosomes
disappears condense, and
become visible
telophase 3-D view of spindle
centrioles
at pole
microtubule
fibres
equatorial
plate
nucleolus and
nuclear envelope nuclear
reappear metaphase envelope
spindle forms breaks down
centromeres separate
anaphase
chromatids joined
by centromere
and attached to
spindle at equator
chromatids
pulled apart
by microtubules
▲ Figure 5.8 Mitosis in an animal cell
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In prophase the chromosomes become visible as long thin threads. During interphase
the DNA had been extended to allow for activity of the genes and for replication. Now,
in nuclear division, the DNA must become tightly packed for the chromosomes to
move about and to separate. They increasingly shorten and thicken by a process of
5
supercoiling. Only at the end of prophase is it possible to see that the chromosomes
consist of two chromatids held together at the centromere. At the same time, the
nucleolus gradually disappears and the nuclear envelope breaks down. In animals,
the centrosome divides and the two centrioles replicate (make copies) to form two
centrosomes.

In metaphase the two centrosomes move to opposite ends of the cell. Microtubules of
the cytoplasm start to form into a spindle, radiating out from the centrioles (page 19).
Each pair of chromatids is attached to a microtubule of the spindle and is arranged at
the equator of the spindle. (Note: in plant cells, a spindle of exactly the same structure is
formed but without the presence of the centrosomes).
In anaphase the centromeres separate, the spindle fibres shorten and the chromatids
are pulled by their centromeres to opposite poles. Once separated, the chromatids are
referred to as chromosomes.
In telophase a nuclear envelope reforms around both groups of chromosomes at
opposite ends of the cell. The chromosomes ‘decondense’ by uncoiling, becoming
chromatin again. The nucleolus reforms in each nucleus. Interphase follows division of
the cytoplasm.
Questions 6 As the contents of a nucleus in the human body prepares to undergo mitosis, how
many chromatids does it contain?
7 Using slides they had prepared to observe chromosomes during mitosis in a plant
root tip, five students observed and recorded the number of nuclei at each stage in
mitosis in 100 cells.
Stage of Number of nuclei counted

mitosis Student 1 Student 2 Student 3 Student 4 Student 5
Prophase 64 70 75 68 73
Metaphase 13 10 7 11 9
Anaphase 5 5 2 8 5
Telophase 18 15 16 13 13
a Calculate the mean percentage of dividing cells at each stage of mitosis. Present
your results as a pie chart.
b Assuming that mitosis takes about 60 minutes to complete in this species of
plant, deduce what these results imply about the lengths of the four steps?
Observing chromosomes during mitosis

Figure 5.8 includes electron micrographs of the main stages of mitosis in actively
dividing animal cells. Note that the centrioles observed in these images will be absent if
you are observing plant cells.
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SUMMARY
5 » The nucleus controls the activities of the cell code for particular polypeptides and are called
throughout life. It is the location of the hereditary genes.
material which is passed from generation to » Replication of the DNA of the chromosomes
generation in reproduction. The division of the occurs in the interphase of the cell cycle when the
nucleus is the first step in cell division. chromosomes are less coiled, well before nuclear
» Chromosomes occur in the nucleus but are only division occurs.
visible, when stained, at times of nuclear division. » Each time the DNA of the chromosomes is copied
The number of chromosomes per nucleus in each (replicated) prior to mitosis and cell division, a part
species is fixed. Chromosomes occur in pairs and of the end of the DNA molecules of chromosomes
have a characteristic shape. is lost. Ultimately, chromosomes would lose genes
» Mitosis is the replicative nuclear division in which, or parts of genes by this process, if they were not
after cell division, the nucleus present in each of protected by the presence of telomeres. Telomeres
two daughter cells formed has exactly the same are long, seemingly disposable non-coding
number of chromosomes as the parent cell, sequences of nucleotide bases at the ends of the
typically two of each type. It is in the diploid (2n) DNA molecules of chromosomes that fulfil this
state. Mitosis is associated with cell divisions of important function.
growth and asexual reproduction. » Mutations are unpredictable changes in the
» Nucleic acids are long, thread-like macromolecules genetic make-up of a cell involving the sequence of
with a uniform and unvarying ‘backbone’ of particular bases at one location (gene mutation).
alternating sugar and phosphate molecules. » Cancers are initiated when cells start to divide
Attached to each sugar molecule is a nitrogenous repeatedly, by mitosis, without control or
base which projects sideways. Since the bases regulation. An irregular mass of cells is formed,
vary, they represent a unique sequence that called a tumour. There are many forms of the
carries the coded information held by the nucleic disease, affecting different tissues of the body.
acid. Often cancers are the result of numerous
» DNA exists as two strands arranged as a double chance mutations triggered by agents known
helix. It occurs in the chromosomes in a highly as carcinogens. These include ionising radiation,
coiled state, supported by a protein framework. tobacco smoke.
Within a chromosome, specific lengths of the DNA

1 a When does mitosis occur in the life cycle of an animal from its development
from a fertilised egg cell until the point when it forms gametes? [2]
b What do you understand by the ‘cell cycle’? [2]
c By means of fully annotated diagrams explain the
difference between the phases of the cycle and the
events that characterise each phase. [12]
d What changes occur during the phases of the cell
cycle to
i the volume of a cell
ii the quantity of DNA during the phases of the
cell cycle? [4]
[Total: 20]
2 a Explain how uncontrolled cell division can result in the formation of a tumour.
b What do you understand by non-malignant and malignant tumours?
c Outline the range of factors that can increase the chances of cancerous
growths.
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3 a As part of a study of the mitotic cell cycle, a student made stained sections of a
root tip of onion, Allium cepa, and observed them with a light microscope.
The student made drawings of six of the cells, A to F, using the high power of 5
the microscope, as shown in Fig. 3.1.
A D

B E
C F
▲ Fig. 3.1
i Complete Table 3.1 to show the sequence of stages in the mitotic cell cycle,
using the letters, A to F, as shown in Fig. 3.1. [1]
Sequence of stages Cell

1 A
2
3
4
5
6
▲ Table 3.1
ii Table 3.2 shows some events that occur during the mitotic cell cycle in
A. cepa.
Complete Table 3.2 by naming the stage of the cell cycle when each event
occurs. [4]
Name of the stage in the

Event in the cell cycle cell cycle
DNA replication
Division of centromeres
Condensation of chromatin
Contraction of spindle fibres
Organisation of chromosomes at the equator Metaphase
▲ Table 3.2
[Total: 5]
(Cambridge International AS and A Level Biology 9700 Paper 23 Q6 a Oct/Nov 2018)
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AS LEVEL
6 Nucleic acids and protein

synthesis
Nucleic acids have roles in Learning outcomes

the storage and retrieval of
genetic information and in
the use of this information 6.1.1 describe the structure of nucleotides, including the phosphorylated
to synthesise polypeptides. nucleotide ATP (structural formulae are not expected)
DNA is the molecule of 6.1.2 state that the bases adenine and guanine are purines with a double ring
heredity and is an extremely structure, and that the bases cytosine, thymine and uracil are pyrimidines
stable molecule that with a single ring structure (structural formulae for bases are not
cells replicate with great expected)
accuracy. The genetic code
explains how the sequence
6.1.3 describe the structure of a DNA molecule as a double helix, including: the
of nucleotides in DNA and importance of complementary base pairing between the 5′ to 3′ strand
messenger RNA (mRNA) and the 3′ to 5′ strand (antiparallel strands), differences in hydrogen
determines the sequence of bonding between C–G and A–T base pairs and linking of nucleotides by
amino acids that make up a phosphodiester bonds
polypeptide. In eukaryotes 6.1.4 describe the semi-conservative replication of DNA during the S phase
this involves the processes of the cell cycle, including: the roles of DNA polymerase and DNA ligase
of transcription in the (knowledge of other enzymes in DNA replication in cells and different
nucleus to produce mRNA,
types of DNA polymerase is not expected) and the differences between
followed by translation in
leading strand and lagging strand replication as a consequence of DNA
the cytoplasm to produce
polypeptides. polymerase adding nucleotides only in a 5′ to 3′ direction
6.1.5 describe the structure of an RNA molecule, using the example of
messenger RNA (mRNA)
Starting point
★ Understanding the structure of nucleic acids allows an understanding of their
role in the storage of genetic information and how that information is used in
the synthesis of proteins.
6.1 Structure of nucleic acids and replication of DNA

Nucleic acids – the information molecules
Nucleic acids are the information molecules of cells; they are the genetic material of all
living organisms and also of viruses. Within the structure of nucleic acid are coded the
‘instructions’ that govern all cellular activities. This code (known as the genetic code) is
a universal one – it makes sense in all organisms.
There are two types of nucleic acids found in living cells, deoxyribonucleic acid
(DNA), and ribonucleic acid (RNA). DNA is the genetic material and occurs in the
chromosomes of the nucleus. But, while some RNA also occurs in the nucleus, most is
found in the cytoplasm – particularly in the ribosomes. Both DNA and RNA have roles
in the day-to-day control of cells and organisms, as we shall see shortly.
Nucleic acids are giant molecules known as macromolecules. Chemically they are
described as polymers because they are made by linking together smaller building
blocks called monomers. These smaller molecules that make up DNA and RNA are the
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nucleotides, and it is these molecules that are condensed together to form long, thread-
like nucleic acids. First you will look at the structure of the nucleotides, themselves.
6
Nucleotides – the building blocks
A nucleotide consists of three components combined together:
» a nitrogenous base, either cytosine (C), guanine (G), adenine (A), thymine (T) or
uracil (U)
» a pentose sugar, either deoxyribose (in DNA) or ribose (in RNA)
» phosphate.

The nitrogenous bases are derived from one of two parent compounds, purine or
pyrimidine. The purine bases are adenine or guanine; the pyrimidine bases are
cytosine, thymine or uracil. These molecules are illustrated in Figure 6.1. You do not
need to know their structural formulae. However, you should note that purines have
a double ring structure and pyrimidines have a single ring structure. We will note the
special significance of this size difference, shortly. It has become traditional in biology to
abbreviate the names of these five bases to their first letters, A, G, C, T and U.
Question
The three components, nitrogenous base, pentose sugar and phosphate, are
1 Distinguish between combined by condensation reactions to form a nucleotide with the formation
a ‘nitrogenous base’ of two molecules of water. The structure of these components and how they are
and a ‘base’ found in combined together are illustrated in Figure 6.1. Here a diagrammatic way of
inorganic chemistry.
representation has been used to emphasise their spatial arrangement.
the components:
phosphate pentose sugars
OH ribose deoxyribose
Pi O P OH CH 2OH OH CH 2OH OH
O O
O
H H H H
H
H H H H
OH OH OH H
nitrogenous bases
adenine guanine thymine uracil cytosine
NH 2 O O NH2
H
N N N
N NH 2 H N CH3 H N N
N O O O
N N N N N N
H O H H H
purine bases pyrimidine bases
condensation to form a nucleotide:
phosphate shown diagrammatically as:

OH H 2O
H 2O Pi phosphate
O P OH Pi
OH O
OH N sugar (pentose) + 2H2O
OH H N NH 2
O
nucleotide
base base
OH OH
ribose
▲ Figure 6.1 The components of nucleotides
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ATP – a nucleotide with unusual features
6 Energy made available within the cytoplasm may be transferred to a molecule called
adenosine triphosphate (ATP). This substance occurs in all cells at a concentration of
0.5–2.5 mg cm−3. It is a relatively small, soluble organic molecule – a nucleotide, which
carries three phosphate groups linked together in a linear sequence (Figure 1.23, page 22).
Look at Figure 1.23 now.
ATP is formed from adenosine diphosphate (ADP) and a phosphate ion (Pi) by transfer
of energy from other reactions. ATP is referred to as ‘the universal energy currency’
because, like money, it can be used in different contexts, and it is constantly recycled.
ATP contains a good deal of chemical energy locked up in its structure. What makes
ATP special as a reservoir of stored chemical energy is its role as a common intermediate
between energy-yielding reactions and energy-requiring reactions and processes.
Energy-yielding reactions include the photophosphorylation reactions of photosynthesis
Direction in the nucleic (page 279), and many of the reactions of cell respiration (page 248).
acid molecule:
in a nucleic acid molecule, Energy-requiring reactions include the synthesis of cellulose from glucose, the synthesis
the phosophate groups are of proteins from amino acids and the contraction of muscle fibres.
bridges between carbon-3 of
one sugar molecule and The free energy available in ATP is approximately 30–34 kJ mol−1, made available in
carbon-5 of the next. the presence of a specific enzyme, referred to as ATPase. Some of this energy is lost as
Consequently, we can identify heat in a reaction, but much free energy is made available to do useful work, more than
direction in the nucleic acid sufficient to drive a typical energy-requiring reaction of metabolism.
molecule, indicating one end
as 5’ and the other end as 3’. » Sometimes ATP reacts with water (a hydrolysis reaction) and is converted to ADP and
Pi. Direct hydrolysis of the terminal phosphate groups like this happens in muscle
5’ Pi
contraction, for example.
» Mostly, ATP reacts with other metabolites and forms phosphorylated intermediates,
making them more reactive in the process. The phosphate groups are released later, so
H2O + both ADP and Pi become available for reuse as metabolism continues.
Pi
Nucleotides become nucleic acid

H2O + Nucleotides themselves then combine together, one nucleotide at a time, to form huge
Pi molecules called nucleic acids or polynucleotides. This occurs by a condensation
reaction between the phosphate group of one nucleotide and the sugar group of another
nucleotide.
H2O +
Pi Figure 6.2 shows how this condensation reaction results in the formation of a covalent
phosphodiester bond between adjacent nucleotides.
H2O + ...shown diagrammatically as:
Pi
Pi
Pi Pi
H2O +
condensation
Pi + H 2O
Pi
+
H2O +
3’ etc. nucleotide + nucleotide dinucleotide
When the polynucleotide ▲ Figure 6.2 A condensation reaction between two nucleotides forms a phosphodiester
chain grows by addition of bond
another nucleotide, the
nucleotides are always added Up to 5 million nucleotides, condensed together, form a polynucleotide. So, nucleic
to the 3’ end. acids are very long, thread-like macromolecules with alternating sugar and phosphate
molecules forming the ‘backbone’. This part of the nucleic acid molecule is uniform and
▲ Figure 6.3 Direction in unvarying. However, also attached to each of the sugar molecules along the strand is one
the nucleic acid molecule
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of the bases, and these project sideways. Since the bases vary, they represent a unique
sequence that carries the coded information held by the nucleic acid.
Figure 6.3 shows how new nucleotides are added to 3′ end of the developing 6
polynucleotide chain, with the phosphate groups acting as a bridge between the carbon-3
of one nucleotide and the carbon-5 of another. In this way, we can identify the direction
of nucleic acid molecules. The existence of direction in DNA strands becomes important
in replication and also when the genetic code is transcribed into messenger RNA.
Introducing DNA

The DNA molecule consists of two antiparallel polynucleotide strands, paired together.
In Figure 6.4 you can see that one chain runs from 5′ to 3′ while the other runs from
3′ to 5′ – which is what ‘antiparallel’ means. These strands are held by hydrogen
bonds between their paired bases. The two strands are of the order of several million
nucleotides in length and they take the shape of a double helix. In all DNA molecules
the nucleotides contain deoxyribose.
Complementary base pairing
The other chemical feature that distinguishes DNA from RNA is the organic bases
present and the way they pair up. In DNA the nitrogenous bases are cytosine (C),
guanine (G), adenine (A) and thymine (T), but never uracil (U). The pairing of bases is
between adenine and thymine (A and T) and between cytosine and guanine (C and G).
This is because there is just enough space between the two sugar–phosphate backbones
for one purine and one pyrimidine molecule. So a purine in one strand must be opposite
a pyrimidine in the other, and vice versa. These are the only combinations that fit
together along the helix. Pairing of bases is accompanied by the formation of hydrogen
bonds; two are formed between adenine and thymine and three are formed between
▼ Figure 6.4 The structure cytosine and guanine. This pairing, known as complementary base pairing, also
of DNA makes possible the very precise way that DNA is copied in a process called replication.
DNA of two polynucleotides in the chromosomes, the helical structure of DNA
held together by hydrogen bonds 3’ is stabilised and supported by proteins
between adjacent bases deoxyribose
phosphate (forms a
adenine thymine Pi phosophodiester bond
Pi
between the nucleotides)
5’
Pi thymine adenine Pi
A links with T
(with 2 H-bonds)
complementary
cytosine guanine Pi base pairs
Pi
C links with G
(with 3 H-bonds)
Pi adenine thymine Pi
CH2OH OH
O
Pi thymine adenine Pi
HO 5’
deoxyribose
Pi guanine cytosine Pi
the DNA molecule is twisted

3’ into a double helix
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EXTENSION
6 The existence of the DNA double helix was discovered, and the way DNA holds
information was suggested by Francis Crick and James Watson in 1953, for which a
Nobel Prize was awarded (Figure 6.5).
Francis Crick (1916–2004) and James Watson (1928–) laid the foundations of a new
branch of biology – cell biology – and achieved this while still young men. Within
two years of their meeting in the Cavendish Laboratory, Cambridge (1951), Crick and
Watson had achieved their understanding of the nature of the gene in chemical terms.
Crick and Watson brought together the experimental results of many other workers,
and from this evidence they deduced the likely structure of the DNA molecule.
» Erwin Chargaff measured the exact amount of the four organic bases in samples
of DNA, and found the ratio of A : T and of C : G was always close to 1. Chargaff’s
results suggest c onsistent base pairing in DNA from different organisms.
Ratio of bases in DNA samples

Organism Adendine : Thymine Guanine : Cytosine
Cow 1.04 1.00
Human 1.00 1.00
Salmon 1.02 1.02
Escherichia coli 1.09 0.99
» Rosalind Franklin and Maurice Wilkins produced X-ray diffraction patterns by

bombarding crystalline DNA with X-rays.
Crick and Watson concluded that DNA is a double helix consisting of:
» two polynucleotide strands with nitrogenous bases stacked on the inside of the
helix (like rungs on a twisted ladder)
» parallel strands held together by hydrogen bonds between the paired bases (A–T, C–G)
» ten per turn of the helix
» two antiparallel strands of a double helix.
They built a model. See Figure 6.4 for a simplified model of the DNA double helix.
a) Watson and Crick with their demonstration model b) Rosalind Franklin produced the c) X-ray diffraction pattern of DNA
of DNA key X-ray diffraction pattern of DNA
at Kings College, London
▲ Figure 6.5 The discovery of the role of DNA
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Replication – how DNA copies itself
Some features of the DNA of the chromosome and how it is copied or replicated have
already been established.
6
» Replication must be an extremely accurate process since DNA carries the genetic
message.
» Replication is quite separate from cell division, for replication of DNA takes place in
the nucleus during interphase – during the S phase of the cell cycle (see Figure 5.5,
page 112) – well before the events of nuclear division.
» Strands of the DNA double helix are built up individually from free nucleotides. The

structure of nucleotides is shown in Figure 6.1.
Before nucleotides can be replicated, the DNA double helix has to unwind and the hydrogen
bonds holding the strands together must be broken, allowing the two strands of the helix to
separate. The enzyme helicase brings about the unwinding process and holds the strands
apart for replication to occur.
Replication forks and the system of enzymes involved in replication

Replication is actually initiated at many points along the DNA double helix. These points
are known as replication forks. Here, the DNA strands separate (a ‘bubble’ forms),
brought about by the enzyme helicase. Then, single-strand binding proteins attach and
prevent the separated strands from repairing. The unwound sections of both strands are
now ready to act as templates for the synthesis of complementary DNA strands.
Both strands are replicated simultaneously. However, since DNA polymerase can add
nucleotides only to the free 3′ end, the DNA strands can elongate only in the 5′ → 3′
direction. Consequently, the details of the replication process differ in the two strands.
Figure 6.6 illustrates the steps.
replication is initiated at many here the DNA double helix is shown uncoiled
points for clarity, although DNA is held uncoiled by
helicase only in the regions of active DNA
antiparallel 5’ 3’ direction replication (the replication forks)
strands of replication
3’ 5’
5’ 3’
parent DNA 5’ 3’ direction

of replication
ultimately, all
replication
forks join up
3’ DNA polymerase ‘pool’ of free

(adds nucleotides) nucleotides
5’
nucleotides attach
by base pairing
helicase
(uncoils DNA)
3’
3’
replication fork
fragments
5’
5’
DNA ligase (seals

fragments)
3’
5’ DNA polymerase
▲ Figure 6.6 DNA replication

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Question The leading strand
6 2 Why are many

replication forks
The exposed 5′ → 3′ strand is referred to as the leading strand. Here, DNA polymerase
adds nucleotides by complementary base pairing to the free 3′ end of the new strand,
required in the in the same direction as the replication fork. This process proceeds continuously,
replication of a single immediately behind the advancing helicase, as fresh template is exposed. The initial
strand of DNA? nucleotide chain formed is actually a short length of RNA called a primer. Then the new
DNA starts from the 3′ end of the RNA primer.
The lagging strand

In contrast to events in the leading strand, here the replication is discontinuous. A series
of relatively short lengths of DNA (fragments) are formed, each one primed separately.
So, first an RNA primer is formed, then DNA polymerase attaches nucleotides to it,
forming a fragment. Next, DNA polymerase replaces the RNA nucleotides at the start
of each fragment with DNA nucleotides. Finally, the enzyme DNA ligase joins the
fragments together.
In this way, short lengths of DNA are synthesised and joined together.
Crick and Watson suggested replication of DNA would be ’semi-conservative’, and this has since been
shown experimentally, using DNA of bacteria ‘labelled’ with a ‘heavy’ nitrogen isotope.
In semi-conservative replication
one strand of each new double helix
comes from the parent chromosome original
and one is a newly synthesised strand (parent)
(i.e. half the original molecule is conserved). DNA
first generation
DNA
second generation
DNA
If an entirely new double helix were

formed alongside the original, then
one DNA double helix molecule
would be conserved without parent DNA
unzipping in the next generation
(i.e. conservative replication).
first generation
DNA
second generation
DNA
▲ Figure 6.7 Semi-conservative versus conservative replication

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EXTENSION
6
The evidence for semi-conservative replication of DNA
By semi-conservative replication we mean that in each DNA molecule formed, one strand is new and one strand
is from the original DNA molecule – so is ‘old’. On the other hand, if replication was ‘conservative’, then one DNA
molecule formed would be of two new strands and the other molecule would consist of the two originals strands.
The confirmation that DNA is replicated semi-conservatively came from an investigation by Meselson and Stahl. In
this experiment, a culture of a bacterium (Escherichia coli, page 2) was grown in a medium (food source) where the

available nitrogen contained only the heavy nitrogen isotope (nitrogen-15, 15N) for many generations. The DNA of
the bacterium became entirely ‘heavy’ as a result.
These bacteria were then transferred to a medium of the normal (light) isotope (nitrogen-14, 14N). The result was
that the new DNA manufactured by the cells was now made of nitrogen-14. The experimenters then observed
and measured the change in concentration of nitrogen-15 and nitrogen-14 in the DNA of succeeding generations.
Note that these observations were possible because the bacterial cell divisions in a culture of E. coli are naturally
synchronised; every 60 minutes they all divide. The DNA was extracted from samples of the bacteria from each
succeeding generation and the DNA in each sample was separated.
Separation of DNA was carried out by placing each sample on top of a salt solution of increasing density in a
centrifuge tube. On being centrifuged, the different DNA molecules were carried down to the level where the
salt solution was of the same density. Thus, DNA with ‘heavy’ nitrogen ended up nearer the base of the tubes,
whereas DNA with ‘light’ nitrogen stayed near the top of the tubes. Figure 6.8 shows the results that were
obtained.
1 Meselson and Stahl ‘labelled’ nucleic acid
(i.e. DNA) of the bacterium Escherichia coli with
‘heavy’ nitrogen (15N), by culturing in a medium
where the only nitrogen available was as 15NH4+ position of heavy (15N) DNA
ions, for several generations of bacteria. 15N DNA
2 When DNA from labelled cells was

extracted and centrifuged in a density
gradient (of different salt solutions) all
the DNA was found to be ‘heavy’.
position of light (14N) DNA
14
N DNA
3 In contrast, the DNA extracted from
cells of the original culture (before
treatment with15N) was ‘light’.
4 Then a labelled culture of E.coli was switched after one generation

back to a medium providing unlabelled nitrogen
only, i.e. 14NH4+. Division in the cells was
synchronised, and:
· after one generation all the DNA was of
intermediate density (each of the daughter
cells contained (i.e. conserved) one of the
parental DNA strands containing 15N alongside
a newly synthesised strand containing DNA after two generations
made from 14N)
· after two generations 50% of the DNA was
intermediate and 50% was ‘light’. This too
agreed with semi-conservative DNA replication,
given that labelled DNA was present in only
half the cells (one strand per cell). increasing density
▲ Figure 6.8 Experiment to show that DNA replication is semi-conservative
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DNA polymerase also has a role in proofreading the new strands. Any ‘mistakes’
that start to happen (such as the wrong bases attempting to pair up) are immediately
6 corrected so that each new DNA double helix is exactly like the original. Then each pair
of double strands winds up into a double helix. The outcome is that one strand of each
new double helix came from the parent chromosome and one is a newly synthesised
strand. This arrangement known as semi-conservative replication because half the
original molecule is conserved.
Introducing RNA
The RNA molecule is relatively short in length, compared with DNA. In fact, RNAs
tend to be between one hundred and one thousand nucleotides long, depending on the
particular role they have. In all RNA molecules the nucleotides contain ribose.
The other chemical feature that distinguishes RNA is that the bases are cytosine (C), guanine
(G), adenine (A) and uracil (U), but never thymine (T). RNA occurs as a single strand.
In the ‘information business’ of cells there are two functional types of RNA. These are
messenger RNA (mRNA – Figure 6.9) and transfer RNA (tRNA). Their roles are in
the transfer of information from the nucleus to the cytoplasm and in the construction
of proteins at the ribosomes, located in the cytoplasm. We will return to this process,
shortly.
sugar–phosphate backbone
Pi
adenine
Pi
uracil
Pi single strand of
polynucleotide
guanine with ribose sugar
and nitrogenous
bases: adenine,
CH2OH OH
O Pi uracil, guanine
and cytosine
cytosine
HO OH Pi
ribose
guanine
Figure 6.9 The structure
of mRNA
DNA RNA
Length Very long strands, several million Relatively short strands
nucleotides long
Sugar Deoxyribose Ribose
Bases C, G, A and T (not U) C, G, A and U (not T)
Forms Consists of two polynucleotide strands Consists of single strands and
in the form of a double helix with exists in two functional forms:
complementary base pairs: » messenger RNA (mRNA)
» C with G and A with T » transfer RNA (tRNA).
» held by hydrogen bonds.
▲ Table 6.1 The differences between DNA and RNA
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6.2 Protein synthesis
Learning outcomes 6
6.2.1 state that a polypeptide is coded for by a gene and that a gene is a
sequence of nucleotides that forms part of a DNA molecule
6.2.2 describe the principle of the universal genetic code in which different
triplets of DNA bases either code for specific amino acids or correspond to
start and stop codons

6.2.3 describe how the information in DNA is used during transcription
and translation to construct polypeptides, including the roles of: RNA
polymerase, messenger RNA (mRNA), codons, transfer RNA (tRNA),
anticodons and ribosomes
6.2.4 state that the strand of a DNA molecule that is used in transcription is
called the transcribed or template strand and that the other strand is
called the non-transcribed strand
6.2.5 explain that, in eukaryotes, the RNA molecule formed following
transcription (primary transcript) is modified by the removal of non-
coding sequences (introns) and the joining together of coding sequences
(exons) to form mRNA
6.2.6 state that a gene mutation is a change in the sequence of base pairs in a
DNA molecule that may result in an altered polypeptide
6.2.7 explain that a gene mutation is a result of substitution or deletion or
insertion of nucleotides in DNA and outline how each of these types of
mutation may affect the polypeptide produced
Starting point
★ The genetic code specifies the amino acids that are assembled to make
polypeptides. The way that DNA codes for polypeptides is central to our
understanding of how cells and organisms function.
DNA and the genetic code

In effect, the role of DNA is to instruct the cell to make specific polypeptides and
proteins. The huge length of the DNA molecule in a single chromosome carries the
codes for a very large number of polypeptides. Within this extremely long molecule, the
relatively short length of DNA that codes for a single polypeptide is called a gene.
Polypeptides are very variable in size and, therefore, so are genes. A very few genes are as
short as 75–100 nucleotides long. Most are at least one thousand nucleotides in length,
and some are more.
Polypeptides are built up by condensation of individual amino acids (Figure 2.20,
page 49). There are only 20 or so amino acids which are used in protein synthesis; all
cell proteins are built from them. The unique properties of each protein lie in:
» which amino acids are involved in its construction
» the sequence in which these amino acids are joined.
The DNA triplet code

The DNA code is in the form of a sequence of the four bases, cytosine (C), guanine (G),
adenine (A) and thymine (T). This sequence dictates the order in which specific amino
acids are assembled and combined together.
Three bases form a base triplet that codes for a specific amino acid. That triplet will code
for the same amino acid in almost all organisms, making it a universal genetic code.
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The code lies in the sequence in one of the two strands of the DNA double helix. This is
called the coding strand. The other strand is complementary to the coding strand. The
6 coding strand is always read in the same direction (from 5′ → 3′).
Despite the fact that there are only four ‘letters’ to the base code ‘alphabet’ with which to
code 20 amino acids, it was immediately clear that combinations of three bases would
be the most likely to code for the amino acids (Figure 6.10). The reason for this is shown
in Table 6.2.
DNA contains four bases: Adenine, Thymine, Guanine, Cytosine.

These are the alphabet of the code.

If one base = one amino acid (singlet code), 4 amino acids can be coded.
If two bases = one amino acid (doublet code), 42 (= 16) amino acids can be coded.
If three bases = one amino acid (triplet code), 43 (= 64) amino acids can be coded.
If four bases = one amino acid (quadruplet code), 44 (= 256) amino acids can be coded.
Conclusion
While the doublet code has too few combinations to code for 20 amino acids, the triplet
code has too many (44 ‘spares’).
Each sequence of three bases
» in DNA is called a triplet code
» in messenger RNA is called a codon
» in transfer RNA is called an anticodon.
It has been found that some triplet codes are punctuations (signifying a stop or the end of
a gene) and some amino acids are coded by more than one triplet code.
▲ Table 6.2 The case for a triplet code
part of the DNA DNA base sequence

molecule of a P is read in one
P complementary reference strand
chromosome direction only
T A S strand (coding strand)
S
(complementary to
P the coding strand)
S C G S
P
T A
P
S G C S
P the triplet code
C G
C G for serine (Ser)
S S
P P
part of a gene T A
S
P P
S S
T A G C
P
S G C S
the triplet code
P A T
P for aspartic acid (Asp)
S C G S
P C G
S T A
S
P
P
part of the amino acid sequence
S
P of a particular protein which the
P gene codes for
C G S
S
P the genetic information
T A S of the coding strand:
S
it specifies the linear
P P sequence of amino acids
G C S
S that make up a protein
▲ Figure
S
TT 6.10
A SPart of a gene and how its DNA codes for amino acids
130 P P
SS
P P
S C G S
482876_06_Biology_120-141.indd 130 P 20/02/20 1:06 PM
So the fact that the code was a three-base one was first deduced. Since then
experiments have established that the code is a three-base or triplet code. Each
sequence of three of the four bases codes for one of the 20 amino acids. 6
Most amino acids have two or three similar codons that code for them (Figure 6.11). The
DNA triplet code ‘TAC’ codes for the amino acid methionine. It is always the first triplet
code of a gene, so a polypeptide starts with this amino acid. Methionine acts as the ‘start’
code – the signal that the polypeptide starts with this amino acid. The start code amino
Amino acid Abbreviation acid methionine is then removed from the polypeptide as part of the changes that occur
forming the protein’s secondary and tertiary structure. Three of the DNA triplet codes are
alanine Ala

stop codes, as we shall see.
arginine Arg
asparagine Asn Second base
aspartic acid Asp A G T C
cysteine Cys AAA Phe AGA Ser ATA Tyr ACA Cys
glutamine Gln AAG Phe AGG Ser ATG Tyr ACG Cys
glutamic acid Glu A
AAT Leu AGT Ser ATT Stop ACT Stop
glycine Gly AAC Leu AGC Ser ATC Stop ACC Trp
histidine His GAA Leu GGA Pro GTA His GCA Arg
isoleucine Ile GAG Leu GGG Pro GTG His GCG Arg
leucine Leu G
GAT Leu GGT Pro GTT Gln GCT Arg
First base
lysine Lys GAC Leu GGC Pro GTC Gln GCC Arg
methionine Met TAA Ile TGA Thr TTA Asn TCA Ser
phenylalanine Phe TAG Ile TGG Thr TTG Asn TCG Ser
T
proline Pro TAT Ile TGT Thr TTT Lys TCT Arg
serine Ser TAC Met TGC Thr TTC Lys TCC Arg
threonine Thr CAA Val CGA Ala CTA Asp CCA Gly
tryptophan Trp CAG Val CGG Ala CTG Asp CCG Gly
C
tyrosine Tyr CAT Val CGT Ala CTT Glu CCT Gly
valine Val CAC Val CGC Ala CTC Glu CCC Gly
▲ Figure 6.11 The amino acids used in proteins and their DNA triplet codes
Protein synthesis – the stages

So, in the working eukaryotic cell, the information in DNA dictates the structure of
polypeptides and proteins, many of which form the enzymes in metabolic process.
There are three stages to the process.
Stage one: transcription

This occurs in the nucleus. A complementary copy of the code is made by the building
of a molecule of messenger RNA (mRNA). In the process, the DNA triplet codes are
transcribed into codons in the messenger RNA. This process is called transcription.
It is catalysed by the enzyme RNA polymerase (Figure 6.12, overleaf).
In transcription, the DNA double helix first unwinds and the hydrogen bonds are
broken at the site of the gene being transcribed. There is a pool of free nucleotides
nearby. Then, one strand of the DNA molecule, the transcribed strand, is the
template for transcription (the other strand is the non-transcribed strand). This
occurs by complementary base pairing. First, the enzyme RNA polymerase
recognises and binds to a ‘start’ signal. The polymerase enzyme then matches free
nucleotides by base pairing (A with U, C with G), working in the 5′ → 3′ direction.
Note that in RNA synthesis it is uracil which pairs with adenine. Hydrogen bonds
then form between complementary bases, holding the nucleotides in place.
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6
mRNA produced by T pool of free nucleotides
T
transcription – a copy of the (nucleoside triphosphates)
C
A
coded information of a gene T
RNA polymerase T
G
U
causes transcription
C
T
of code into
G
mRNA
T
T
G
T
G
enzyme removes two phosphates from T
A T T
C
nucleotide and links the 5’ end of the nucleotide
C
U
G
to the 3’ end of the growing RNA molecule
free nucleotides align by

base pairing and are held
T
T
C
C
A
A
A
C
A
C
C
C
G
G
G
G
G
coding strand
by hydrogen bonds
5’
3’
5’
U
A
C
A
U
U
C
C
C
G
G
helix re-forms
G 3’
G
T
T
T
C
C
C
A
A
A
C
G
G
G
G
as the RNA
polymerase coding strand read in the
moves along 3’ 5’ direction
mRNA strand
3’
5’
mature mRNA passes out of
the nucleus via pores in
mRNA the nuclear envelope
to ribosomes in
the cytoplasm
5’ pore in nuclear membrane

▲ Figure 6.12 Transcription
Question Each free nucleotide is then joined by a phosphodiester bond between the sugar and the
phosphate groups of adjacent nucleotides of the RNA strand. This is brought about by
3 State the sequence of the action of the enzyme RNA polymerase.
changes catalysed by
RNA polymerase. Once the messenger RNA strand is formed it leaves the nucleus through pores in the
nuclear envelope and passes to tiny structures in the cytoplasm called ribosomes
where the information can be ‘read’ and is used. Then the DNA double stand once more
reforms into a compact helix at the site of transcription.
Post-transcriptional modification of RNA

The Human Genome Project (and similar studies of the genomes of other organisms)
has established the sequence of bases in very many genes. This has led to a discovery
of some non-coding regions in the base sequences of genes. Many of the genes of
eukaryotes have non-coding DNA sequences within their boundaries. The sections of
the gene that carry meaningful information (code for amino acids) are called exons.
The non-coding sequences that intervene – interruptions, in effect – are called introns.
While genes split in this way are very common in higher plants and animals, some
eukaryotic genes contain no introns at all.
When a gene consisting of exons and introns is transcribed into mRNA, the mRNA
formed contains the sequence of introns and exons, exactly as they occur in the DNA.
Now, you can see that, if this unmodified mRNA was to be ‘read’ and transcribed in a
ribosome, it would undoubtedly present problems in the protein-synthesis step.
In fact, an enzyme-catalysed reaction known as post-transcriptional modification
removes the introns as soon as the mRNA has been formed (Figure 6.13); the production
of this enzyme is also under the control of a gene. As a result, the short lengths of
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‘nonsense’ transcribed into the RNA sequence of bases are removed. This is known as
RNA splicing and the resulting shortened lengths of mRNA are described as mature.
It this form of mRNA that passes out into the cytoplasm, to the ribosomes, where it is
involved in protein synthesis.
6
Incidentally, the genes of prokaryotes do not have introns, and the prokaryotic cell does
not have the enzyme machinery to carry out splicing, either. This means, when a genetic
engineer plans to place a copy of a eukaryotic gene in the chromosome of a bacterium,
that copy has to be intron-free.

mRNA produced by
transcription – a copy of the
coded information of a gene
many genes contain short lengths of
‘nonsense’ (sequences of bases additional to
coded information of the gene) called introns
introns are ‘edited’ out of the mRNA

by the action of enzymes present in the
nucleus
introns
exons
what remains, known as exons, are

joined up to form mature mRNA
3’
5’
mature mRNA passes out of the nucleus
via pores in the nuclear membrane
pore in nuclear membrane

to ribosomes in the cytoplasm
▲ Figure 6.13 Post-transcriptional modification
Stage two: amino acid activation

This occurs in the cytoplasm. In stage two, amino acids are activated by combining with
short lengths of a different sort of RNA, called transfer RNA (tRNA). While transfer
RNAs are relatively short, they are long enough to be folded into the shape of a clover
leaf. Their most important feature is that there is a different transfer RNA for each of the
20 amino acids involved in protein synthesis.
So each amino acid has its ‘own’ type of transfer RNA. At one end of each transfer
RNA molecule is a site where the particular amino acid can be joined. The other end
of the transfer RNA molecule is folded into a loop. Here, a sequence of three bases
forms an anticodon. This anticodon is complementary to the codon of messenger
RNA that codes for the specific amino acid.
The amino acid is attached to its transfer RNA by an enzyme. These enzymes, too, are
specific to the particular amino acids (and types of transfer RNA) to be used in protein
synthesis. The specificity of the enzymes is a further way of ensuring the code is
implemented correctly and the amino acids are used in the correct sequence.
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ATP provides the energy for the attachment of amino acid to its specific tRNA.
6
Each amino acid is linked to a specific transfer RNA (tRNA)
before it can be used in protein synthesis. This is the process
of amino acid activation. It takes place in the cytoplasm.
tRNA specific for tRNA–amino

amino acid1 acid1 complex
amino
point of amino
acid1
acid attachment
enzyme1
+ amino + ATP + AMP + 2Pi
acid1
specific
enzyme
Anticodon = three consecutive bases in tRNA,

anticodon specific complementary to a codon on the mRNA
for amino acid1 e.g. AAA is complementary to UUU.
▲ Figure 6.14 Amino acid activation

ribosome moves
along the mRNA
one triplet codon
small subunit
at a time Stage three: translation
In stage three a protein chain is assembled by a process called translation. This occurs
in the ribosome (Figure 6.15).
You can see that the ribosome consists of a large and a small subunit. Both parts of the
ribosome are intimately involved in the process of translation.
» On arrival at the ribosome, the messenger RNA molecule binds to the small subunit
large subunit at an a ttachment site. In this position there are six bases (two codons) of the
▲ Figure 6.15 Ribosome messenger RNA exposed to the large subunit at any time.
structure » The first three exposed bases (codon) of messenger RNA are always AUG. A molecule
of transfer RNA with the complementary anticodon UAC forms hydrogen bonds with
this codon. The amino acid methionine is attached to this transfer RNA molecule.
» A second transfer RNA molecule bonds with the next three bases of the messenger
RNA m olecule, bringing another amino acid alongside the methionine molecule.
Which amino acid this is depends on the second codon, of course.
Question » While the two amino acids are held close together within the ribosome, a peptide
bond is formed between them by condensation reaction. This reaction is catalysed by
4 Draw and label the an enzyme found in the large subunit. A dipeptide has been formed.
structure of a peptide » Now the ribosome moves along the messenger RNA molecule in the 5′ → 3′
bond between two direction and the next codon is read. At the same time, the first transfer RNA
amino acids. molecule (with anticodon UAC) leaves the ribosome, minus its amino acid.
» Then a third transfer RNA molecule bonds with the next codon of the messenger
RNA m olecule, bringing another amino acid alongside the second amino acid
residue of the dipeptide. I mmediately, a peptide bond is formed between them by a
condensation reaction. A tripeptide has been formed and starts to emerge from a hole
within the large subunit.
» Again, the ribosome moves along the messenger RNA molecule and the next codon
is read. At the same time, the second transfer RNA molecule leaves the ribosome,
minus its amino acid.
» A fourth transfer RNA brings another amino acid to lie alongside the third amino
acid residue. While these amino acids are held close together another peptide bond is
Question formed.
5 What different forms » By these steps, constantly repeated, a polypeptide is formed and emerges from
of RNA are involved the large subunit. Eventually a ‘stop’ codon is reached. This takes the form of one
in ‘transcription’ and of three codons – UAA, UAG or UGA. At this point the completed polypeptide is
‘translation’ and what released from the ribosome into the cytoplasm.
are the roles of each?
The steps of translation are shown in Figure 6.17, page 136.
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Where ribosomes occur in cells
Many ribosomes occur freely in the cytoplasm. These are the sites of synthesis of
proteins that are to remain in the cell and fulfil particular roles there. It is common 6
for several ribosomes to move along the messenger RNA at one time; the structure
(messenger RNA, ribosomes and their growing protein chains) is called a polysome
(Figure 6.16).
Other ribosomes are bound to the membranes of the endoplasmic reticulum (known as
rough endoplasmic reticulum, RER) and these are the site of synthesis of proteins that
are subsequently secreted from cells or packaged in lysosomes there.

ribosomes moving mRNA in
along mRNA cytoplasm
ribosome
+
protein
growing polypeptide
chains
▲ Figure 6.16 A polysome
Triplet codes, codons and anticodons

The sequence of bases along DNA molecules is the genetic code. This sequence
ultimately determines the sequence of amino acids from which polypeptides are
constructed.
» The sequence of bases in the DNA molecule is transcribed to a complementary
sequence of bases in messenger RNA. DNA ‘codes’ are referred to as triplet codes
and those in messenger RNA are called codons.
» Free amino acids in the cytoplasm attach to specific transfer RNA molecules. There is
one transfer RNA molecule for each of the twenty different amino acids. The triplet of
bases of a transfer RNA molecule is known as an anticodon.
» In ribosomes, transfer RNA anticodons align with RNA codons by complementary
base pairing. This brings amino acids side by side and peptide bonds are formed
between them. A polypeptide molecule is formed.
By these steps, the DNA code is translated into an amino acid sequence in a polypeptide
(Figure 6.17, overleaf). There are different ways of presenting the genetic code and this
is the significance of the term genetic dictionary. The genetic dictionary is a list of the
particular base sequences that correspond with particular amino acids. It depends on
whether it is the code in DNA, messenger RNA (or transfer RNA) that is quoted.
Can you say why?
The DNA triplet codes are recorded in Figure 6.11 (page 131) while those of messenger
RNA are listed in Figure 6.18 (page 137). These codes do not need memorising but their
relationship is important and you do need to be able to use them.
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ribosome
polypeptide termination of
6
elongation translation
initiation of
translation
3’
‘mature’ 5’
mRNA
position of position of
start codon stop codon
part of mRNA
small subunit
of ribosome
complementary AUG GA AG A A G C U U U U G U U C
codons/anticodons UAC
held by hydrogen codons to
U
bonds CU be ‘read’
large subunit of tRNA–amino

Met
ribosome acid complex
Glu with anticodon
(Glu arriving)
ribosome moving along

mRNA one triplet at a time
A U G G A A G A A G C U U U UG U U C
AAA CAA
CG
A two tRNAs
temporarily held
used tRNA leaving
on ribosome
Phe Val
amino acid
Ala
residues Glu
Glu peptide bond
polypeptide strand Met formed between
being built up amino acids held
peptide bonds
at the ribosome
U U U UG A
AAA
stop codon
used tRNA leaving
peptide bonds
finally, ribosome
and polypeptide
chain released
▲ Figure 6.17 Translation
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Amino acid Abbreviation Second base
alanine
arginine
Ala
Arg
U C A G 6
UUU Phe UCU Ser UAU Tyr UGU Cys
asparagine Asn
UUC Phe UCC Ser UAC Tyr UGC Cys
aspartic acid Asp U
UUA Leu UCA Ser UAA Stop UGA Stop
cysteine Cys
UUC Leu UCG Ser UAG Stop UGG Trp
glutamine Gln
CUU Leu CCU Pro CAU His CGU Arg
glutamic acid Glu

CUC Leu CCC Pro CAC His CGC Arg
glycine Gly C
CUA Leu CCA Pro CAA Gln CGA Arg
First base
histidine His
CUG Leu CCG Pro CAG Gln CGG Arg
isoleucine Ile
AUU Ile ACU Thr AAU Asn AGU Ser
leucine Leu
AUC Ile ACC Thr AAC Asn AGC Ser
lysine Lys A
AUA Ile ACA Thr AAA Lys AGA Arg
methionine Met AUG Met ACG Thr AAG Lys AGG Arg
phenylalanine Phe GUU Val GCU Ala GAU Asp GGU Gly
proline Pro GUC Val GCC Ala GAC Asp GGC Gly
serine Ser G
GUA Val GCA Ala GAA Glu GGA Gly
threonine Thr GUG Val GCG Ala GAG Glu GGG Gly
tryptophan Trp
tyrosine Tyr
valine Val
▲ Figure 6.18 The messenger RNA genetic dictionary
Question 6 A sequence of bases in a sample of messenger RNA was found to be:

GGU, AAU, CCU, UUU, GUU, ACU, CAU, UGU
a What sequence of amino acids does this code for?
b What was the sequence of bases in the coding strand of DNA from which this
messenger RNA was transcribed?
c Within a cell, where are triplet codes, codons and anticodons found?
EXTENSION
DNA also codes for the RNA of cells
The DNA of the chromosomes codes for all the RNA m olecules that a cell contains,
as well as the proteins. There is a different enzyme system that ‘reads’ the DNA that
specifically codes for these RNA molecules, additional to the enzymes that catalyse
the formation of messenger RNA.
Gene mutations
We have seen that a gene is a sequence of nucleotide pairs which codes for a sequence of
amino acids. Normally, the sequence of nucleotides in the DNA is maintained without
changing but, very occasionally, it does. If a change occurs we say a mutation has
occurred.
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A gene mutation involves a change in the sequence of bases of a particular gene.
This change may result in the alteration or non-production of a cell protein,
6 for example. At certain times in the cell cycle mutations are more likely than at
other times. One such occasion is when the DNA molecule is replicating. We
have noted that the enzyme DNA polymerase that brings about the building of a
complementary DNA strand also ‘proof reads’ and corrects most errors. However,
gene mutations can and do occur spontaneously during this step. Also, certain
conditions or chemicals may cause change to the DNA sequence of bases (Table 5.2,
page 115).
How mutations may affect the phenotype

An abrupt change in the structure, arrangement or amount of DNA of chromosomes
may result in a change in the characteristics of an organism (its phenotype) or of
an individual cell. This is because the change, called a mutation, may result in the
alteration or non-production of a cell protein because of a change in the messenger
RNA which codes for it.
Gene mutations can occur spontaneously as a result of errors in normal cell processes
such as DNA replication but this is rare. Alternatively, gene mutations can be caused by
environmental agents we call mutagens. These can include ionising radiation in the
form of X-rays, cosmic rays, and radiation from radioactive isotopes (alpha particles,
beta particles and gamma rays). Any of these can cause breakage of the DNA molecule.
Non-ionising mutagens include UV light and various chemicals, including carcinogens
in tobacco smoke (tar compounds). These act by modifying the chemistry of the base
pairs of DNA. The different ways this may happen are shown in Table 6.2.
Change within the gene Likely impact or effect

Base addition: one or more bases are These bring about frame shifts in the code,
added to a sequence which means that potentially every amino acid
e.g. GAG CCT GAG → GAG TCC TGA G from that point onwards is wrong. This is likely
to be catastrophic to the functioning of the
Base deletion: one or more bases are
protein.
lost from a sequence
(Look up which amino acids this sequence coded
e.g. GAG CCT GAG → GAG CTG AG
for originally in Figure 6.11, page 131. What
does it code for now?)
Often, the effect is to change the properties of
the protein, particularly its tertiary structure
(page 50) – or to cause no protein to be coded
for at all.
Base substitution: one or more bases DND code is said to be degenerate because
are substituted: many amino acids have two or more triplet
e.g. CCT GAG CCT → CCT GTG CCT codes, so a substitution may have no effect as
the correct amino acid may still be coded for.
Alternatively, a substitution may cause an
alternative amino acid to be built into a protein,
changing its tertiary structure and properties.
However, if a substitution results in a ‘stop’
triplet code, then this could also be catastrophic
to the protein’s structure and function.
▲ Table 6.2 Different ways the base sequence in a gene may be altered
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SUMMARY
» Nucleic acids are polymers. They are triplet of bases at one end (known as an anticodon)
6
polynucleotides composed of long chains and a point of attachment for a specific amino acid
of nucleotide monomers (a pentose sugar, a at the other end. The role of transfer RNA is to
phosphate molecule and a nitrogenous base) pick up free amino acids and bring them to the
combined together. There are two forms of nucleic messenger RNA in the ribosome. Complementary
acid, DNA and RNA. These forms differ in the sugar base pairing between the codons of messenger
and in the bases they contain, and in their roles RNA and the anticodons of transfer RNA results

in the cell. DNA is found in the chromosomes and in the original DNA code being translated into an
RNA in both the nucleus and the cytoplasm. DNA amino acid sequence in the process of polypeptide
also occurs in mitochondria and chloroplasts. and protein synthesis.
» ATP is the universal energy currency molecule » There are three stages to polypeptide and protein
by which energy is transferred to do useful synthesis.
work. ATP is a soluble molecule, formed in the — In the nucleus, a copy of the genetic code
mitochondria but able to move into the cytosol by of a gene is made in the form of a single
facilitated diffusion. It diffuses freely about cells. strand of messenger RNA in the stage called
» The sequence of four bases, adenine (A), thymine transcription. The messenger RNA passes out
(T), guanine (G) and cytosine (C), along a DNA into the cytoplasm.
molecule is the genetic code. This is a three-letter — In the cytoplasm amino acid activation occurs.
code – three of the four bases code for a particular Each of the 20 amino acids is attached to a
amino acid. The sequence of bases in the DNA specific transfer RNA molecule.
molecule may be transcribed to a complementary — Finally a new polypeptide is assembled
sequence in messenger RNA (mRNA). Once formed, when the information of the messenger RNA
messenger RNA passes out of the nucleus into is translated (‘read’) in a ribosome and the
the cytoplasm and to a ribosome where polypeptide transfer RNA molecules with their attached
synthesis occurs. DNA ‘codes’ are referred to as amino acids are aligned in the order given in
triplet codes and those in messenger RNA are the code. Peptide bonds are formed between
called codons. the amino acids.
» In eukaryotes, post-transcriptional modification of » A gene mutation involves a change in the sequence
RNA removes introns (non-coding sequences) as of bases of a particular gene. This change may
soon as the mRNA has been formed. result in the alteration or non-production of a cell
» Transfer RNA (tRNA) molecules occur in the protein.
cytoplasm. These molecules have a particular

1 DNA replication is an important event in the cell cycle.
a State when, during the cell cycle, DNA replication occurs. [1]
b Fig. 1.1 shows pairing between two bases, X and Y, in a DNA molecule.
H
X Y
N O H N
N
N H N
N N
N H O
▲ Fig. 1.1
i Name the type of bond shown by the dotted lines between the bases. [1]
ii State which base, X or Y, is a pyrimidine and explain your answer. [1]
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c The compound benzopyrene, found in tar from tobacco smoke, can become
chemically changed in cells and interferes with DNA replication, causing gene
6 mutations.
i State what is meant by the term gene mutation. [2]
ii Mutations that occur in dividing cells of the gas exchange system
may result in lung cancer.
Suggest the differences in the cell cycle of a cancer cell compared with that
of a normal cell of the same type. [2]
[Total: 7]

2 a A gene in the form of a double-stranded length of DNA contains 12 000
nucleotides. Explain the maximum number of amino acids that could be
required to transcribe it. [6]
b What may the triplet codes of a gene represent other than the amino acids of
the polypeptide that it codes for? [2]
c The following is a short sequence of the triplet codes for part of the primary
structure of a polypeptide:
AAA ATA GTA TAA CAC TGC CTC TCG
Give the sequence of codons of mRNA transcribed from this part of the gene,
and the sequence of anti-codons that will base pair with them. [8]
d How does the structure of tRNA differ from that of mRNA? [4]
[Total: 20]
3 A molecule of messenger RNA (mRNA) was produced during the transcription of a
gene. Part of the template sequence of DNA was ATGC.
The diagram shows the part of the molecule of messenger RNA corresponding to
that sequence of four bases.
O D
H H
N
O
H N O
O P O CH2
O
G O H H H H E
N
H H
N N
OH H
O
N N H
O P O CH2
O
O H H
H H N
H H H
N
OH
O
H N O
O P O CH2
O
O H H
O guanine
H H H
F N N
OH H
O H
N N N
O P O CH2
O H
O H H
H H
OH
O
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a Name the parts of the mRNA molecule shown in the diagram above labelled D,
E, F and G. [4]
b Copy and complete the table to show three ways in which mRNA
differs from DNA. [3]
6
mRNA DNA
1
2
3

c Describe the role of mRNA after it leaves the nucleus and enters
the cytoplasm of a eukaryotic cell. [4]
[Total: 11]
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AS LEVEL
Flowering plants do not have Learning outcomes

compact bodies like those
of many animals. Leaves
and extensive root systems 7.1.1 draw plan diagrams of transverse sections of stems, roots and leaves
spread out to obtain the of herbaceous dicotyledonous plants from microscope slides and
light energy, carbon dioxide, photomicrographs
mineral ions and water 7.1.2 describe the distribution of xylem and phloem in transverse sections of
that plants gain from their stems, roots and leaves of herbaceous dicotyledonous plants
environment to make organic
7.1.3 draw and label xylem vessel elements, phloem sieve tube elements and
molecules, such as sugars
and amino acids. Transport
companion cells from microscope slides, photomicrographs and electron
systems in plants move micrographs
substances from where they 7.1.4 relate the structure of xylem vessel elements, phloem sieve tube
are absorbed or produced elements and companion cells to their functions
to where they are stored or
used.
Starting point
★ Plants have two transport tissues: xylem and phloem.
7.1 Structure of transport tissues

Internal transport – the issues
The cells of organisms need a constant supply of water and organic nutrients such
as glucose and amino acids, and most need oxygen. The waste products of cellular
metabolism have to be removed, too. In single-celled organisms and small multicellular
organisms, internal distances (the length of diffusion pathways) are small. Here,
movements of nutrients and other molecules can occur efficiently by diffusion (page 87).
However, some substances must be transported across membranes, such as the cell
surface membrane, by active transport (page 98).
In larger organisms diffusion alone is not sufficient. This is because the amount of
gas an organism needs to exchange is largely proportional to its volume (the bulk of
respiring cells). At the same time, the amount of exchange that can occur is proportional
to the surface area over which diffusion takes place. The surface area to volume ratio
decreases as size increases, as we have seen. Consequently, an internal transport
system is essential. This alone can provide enough of what is required by the cells
in larger and more bulky organisms. Also, the more active an organism is the more
nutrients are likely to be required in cells and so the greater is the need for an efficient
system. Question 2 on page 145 explores these issues of size, shape and mechanisms of
internal transport.
Transport in multicellular plants

The flowering plants are the dominant land plants. Some are trees and shrubs with
woody stems, but many are non-woody (herbacious) plants. Whether woody or
herbaceous, a flowering plant consists of stem, leaves and root.
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Internal transport occurs by mass flow but here there is no pumping organ. Two
separate tissues are involved: water and many ions travel in the xylem, while
manufactured foods (mainly sugar and amino acids) are carried in the phloem. 7
Xylem and phloem are collectively known as the vascular tissue. They occur together in
the centre of roots and in the vascular bundles of stems and leaves of the plant.
The stem
The role of the stem is to support the leaves in the sunlight and to transport organic
materials (mainly sugar and amino acids), ions and water between the roots and leaves.

This transport occurs in the vascular bundles (Figure 7.1). The vascular bundles of the
stem occur in a ring just below the epidermis. To the outside of the vascular bundles
lies the cortex and to the inside is the pith. Both cortex and pith mostly consist of living,
relatively unspecialised cells with thin cellulose walls (Figure 7.6, page 147).
young sunflower plant

with stem and root partly cut open to
show vascular tissue the branching
vascular system of the stem
vascular bundles
termical bud (main growing leaf traces
point of stem)
leaf stalk
lateral leaf blade stem in TS

bud epidermis
phloem
leaf stalk xylem
stem with pith
ring of vascular cortex
vascular
bundle
soil level bundles part of the stem
tissue cut away
main root with cortex pith
central stele of epidermis
region of vascular tissue leaf trace
root hairs vascular bundle
growing point
of roots
cap of fibres – long, narrow,

tapering cells with thickened
walls strengthened with lignin.
These cells are now without living
contents. Fibres, with the rest of phloem tissues on the
the vascular bundle, provide part outside of the vascular
of the mechanical support for the bundle – food-transporting
aerial system (stem, leaves, flowers) tissue, including sugar from
the leaves and amino acids
cambrium (cells
from the root tips
able to divide)
xylem vessels on the inside
of the vascular bundle – their
main role is the passage of
water up the plant
ground tissue
of plant
photomicrograph of TS vascular
bundle and surrounding tissues in
the outer stem of sunflower (ë150)
photomicrograph of sunflower stem in TS (ë30)
▲ Figure 7.1 The distribution and structure of the vascular bundles of the stem
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The leaves
7 The leaf is an organ specialised for photosynthesis – the process in which light energy
is used to make sugar. Carbon dioxide from the air and water from the soil are the raw
materials used, oxygen is the waste product.
The leaf consists of a leaf blade connected to the stem by a leaf stalk. The blade is a
thin structure with a large surface area. Within the leaf blade are mesophyll cells that
are packed with chloroplasts – the organelles in which photosynthesis occurs. There
is a thin film of water on the outer surface of these cells. The epidermis is a tough,
transparent, single layer of cells surrounding the mesophyll tissue. There is an external
waxy cuticle to the epidermis which is impervious. This reduces water vapour loss from
the leaf surface (Figure 7.2).
The epidermis has many tiny pores, called stomata – the sites of gas exchange. Within
the leaf’s mesophyll tissue are continuous air spaces. Throughout the leaf blade is a
network of vascular bundles. These provide mechanical support but the leaf is also
supported by the turgidity of all its cells, surrounded as they are by the tough epidermis.
Leaves are relatively delicate structures and, at times, they have to withstand destructive
forces such as wind and rain.
veins leaf stalk
epidermis with waxy cuticle lateral bud
stem
spongy mesophyll
leaf blade (TS)
palisade mesophyll branching veins of the leaf
form a supportive network
leaf blade
network of lateral veins
water-carrying vessels (xylem)

food-carrying cells epidermis cell, with waxy cuticle
main vein (phloem) thicker outer wall of outer wall
cell wall
nucleus
cytoplasm
vacuole
palisade mesophyll cell,
chief site of photosynthesis
TS leaf blade, HP in the green plant
cell wall
chloroplasts
cytoplasm
vacuole
nucleus
vein, cut in
LS and TS
spongy
mesophyll
air spaces lower epidermis with stomata

▲ Figure 7.2 The structures of the leaf
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The root
The root anchors the plant in the ground and is the site of absorption of water and ions from
the soil. The main tap root forms lateral roots, and growth continues at each root tip. The 7
growing plant is continuously making contact with fresh soil. This is important because the
thin layer of dilute soil solution found around soil particles is where the plant obtains the
Question huge volume of water it requires. Minerals salts as ions are also absorbed from here.
1 Outline the The vascular tissue of the root occurs in a single, central stele. Around the stele is a
properties of single layer of cells, the endodermis. These cells have a waterproof waxy strip made of the
cellulose that make it
substance suberin in their radial walls, known as the Casparian strip. Immediately within

an ideal material for
the endodermis is another single layer of living cells, known as the pericycle (Figure 7.3).
plant cell walls.
Only at the base of the stem is the vascular tissue of the root reorganised into several vascular
bundles arranged around the outside of the stem.
exodermis
soil level cells with
TS mature root of waxy walls
exodermis:
in older parts of the root the buttercup (ë80)
walls of the outermost cells
become waxy (so preventing
water uptake in these regions)
growth at tip
of lateral root lateral roots
occurs in the
same way as at
the tip of the main root of tap
main (tap) root root system endodermis: a single layer of cells with a
region of root waxy strip in their radial walls, apart from an
hairs (water occasional passage cell with walls of cellulose only
uptake from pericycle: a single layer
the soil occurs of cells immediately
here) below the endodermis
region of
elongation (pushes region of growth
root tip through (cell division) at xylem
the soil) root tip
See Figure 7.8
phloem
HP detail of stele at
centre of root (ë450) cortex
▲ Figure 7.3 The structure of the root (cells containing
starch grains)
Question 2 The external dimensions, volume and surface area of six geometrically shaped objects –
three of a compact shape and three that are flat and thin – are listed in the table below.
Compact Flat and thin
Small Medium Large Small Medium Large
Dimensions/mm 1 3 1 3 1 2 3 2 3 2 4 3 4 3 4 2 3 1 3 0.5 8 3 2 3 0.5 16 3 8 3 0.5
Volume/mm3 1 8 64 1 8 64
Surface area/mm2 6 24 96 7 42 280
a Calculate the surface area to volume c Comment on the effect of shape on

ratio of the six objects. the surface area to volume ratio of an
b Comment on the effect of shape on object as the size increases.
the surface area of an object as the d If these objects were organisms, what
size of the object increases. are the implications of their size and
shape on the movement of nutrients
or waste products by diffusion?
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The structure of xylem and phloem tissue
7 Xylem begins as elongated cells with cellulose walls and living contents, connected end
to end.
photomicrograph of xylem tissue in LS drawing of xylem vessels in TS and LS
all vessels TS
have lignin-
free ‘pit’
areas in
their walls
xylem parenchyma
fibre (the only living
cells of xylem
tissue)
LS
lignin thickening as spirals, rings, network

or solid blocks – deposited on inside of
vessel, strengthening the cellulose layers
▲ Figure 7.4 The structure of xylem tissue
fibres During development, the end walls are dissolved away so that mature
TS xylem vessels are long, hollow tubes. The living contents of a developing
xylem vessel are used up in the process of depositing cellulose thickening
to the inside of the lateral walls of the vessel. This is hardened by the
deposition of a chemical substance, lignin. Lignin is a substance that
LS thick wall of makes cross links with the hemicelluloses that fill the gaps between
cellulose
impregnated cellulose fibres. This greatly strengthens the cellulose and makes it
pit in walls
connecting with lignin impermeable to water. Consequently, xylem is an extremely tough tissue.
cells Furthermore, it is strengthened internally, which means it is able to resist
negative pressure (suction) without collapsing in on itself. When you
examine xylem vessels in longitudinal sections by light microscopy, you
will see that they may have differently deposited thickening; many have
rings of thickening, for example (Figure 7.4). Other xylem vessels have
more massive thickenings. However, all xylem vessels have areas in their
empty lumen lateral walls (including the pits where the cellulose wall is especially thin)
of mature in which there is a layer of cellulose but no lignin. Here the walls are
fibres
(dead cells)
entirely permeable and permit lateral movements of water to surrounding
tissues. This is role of the xylem – to supply water to the living cells of the
plant.
Fibres also occur between xylem vessels, thereby strengthening the whole
bundle. Interestingly, in ferns and cone-bearing trees, xylem tissue is
fibres are a thick-walled tissue, with walls of absent. Here the water-conducting tissue consists of fibre-like tracheids
cellulose strengthened by lignin – when mature with large pits in their lateral walls through which water passes from
the cell contents die; fibres are long, narrow,
pointed, empty cells with pits in their walls tracheid to tracheid (Figure 7.5).
where the living contents once connected
▲ Figure 7.5 The structure of fibres
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Phloem tissue consists of sieve tubes and companion cells, and is served by transfer
cells in the leaves. Sieve tubes are narrow, elongated elements that are connected end to
end to form tubes. The end walls, known as sieve plates, are perforated by pores. The
cytoplasm of a mature sieve tube has no nucleus, nor many of the other organelles of a
7
cell. However, each sieve tube is connected to a companion cell by strands of cytoplasm
called plasmodesmata, that pass through narrow gaps (called pits) in the walls. The
companion cells service and maintain the cytoplasm of the sieve tube, which has lost
its nucleus. Phloem is a living tissue, and has a relatively high rate of aerobic respiration
during transport. In fact, transport of manufactured food in the phloem is an active
process, using energy from metabolism (Figure 7.6).

photomicrograph of LS phloem in HP (×200)
phloem is a tissue that may become crushed
and damaged as stem tissue is sectioned for
microscopy
sleve tube
sieve tube with
sieve plate companion cell
sleve plate
in section
sleve plate
in face view
cytoplasmic connections
between companion cells
and sieve tube contents
cytoplasm loses nucleus

and many organelles
phloem tubes are the site of movement of

sugar and amino acids.
▲ Figure 7.6 The structure of phloem tissue
Observing and recording high power detail of cells

The cells of the ground tissues make up the bulk of stem (and root) of herbaceous (non-
woody) plants, around the vascular tissue. These are collenchyma and parenchyma cells,
and they show relatively few structural adaptations. They are concerned with support
due to the turgidity of all the living cells contained within the stem. Starch storage also
occurs here. Fibres are different. Here there are no living contents, but their thickened
walls are impregnated with lignin, and are extremely tough (Figure 7.5).
The outermost layer of the stems (and leaves) of herbaceous plants is a continuous layer
of compact, tough cells, one cell thick, called the epidermis (Figure 7.2). These cells
have a layer of wax deposited on the external walls, and their strength and continuity
provides mechanical support by counteracting the internal pressure due to turgidity.
You will be examining prepared slides of sections through plant organs in the
laboratory, using the light microscope. With guidance, the different types of xylem
vessels, sieve tubes and companion cells, fibres, parenchyma and collenchyma ground
tissue can be identified in longitudinal and transverse sections and their structures
recorded. Follow the guidance on recording observations in drawings on page 6.
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collenchyma parenchyma
TS TS
7 living contents of
cytoplasm
vacuole
nucleus
thick cellulose wall thin cellulose air spaces between

(occurs at corners wall elsewhere living cells
of cells)
TS LS
collenchyma consists of living cells, parenchyma consists of living cells that

quite narrow and elongated in shape show little or no specialisation – when
with unevenly thickened cellulose turgid they exert pressure on the epidermis
walls; it is a highly flexible supporting and thus support the herbaceous stem;
tissue found in leaves and young stems they are the site of starch storage
▲ Figure 7.7 The structure of parenchyma, collenchyma and fibres
Observing and recording plant structure using

low-power plan diagrams
You will be examining prepared slides of sections through plant organs in the
laboratory, using the light microscope. The name given to the detailed study of the
structure of living tissues is Histology. Slides of thin sections were commonly used to
discover the structure of multicellular organisms. You may notice that the material they
show has been selectively stained to highlight structures.
With guidance, the different tissues a slide shows can be identified and their precise
Question distribution represented in a plan diagram (also called a tissue map). This will show
3 Draw and label a their relative positions to scale. Individual cells are not shown. Then the size of the
plan diagram of a specimen can be calculated and the magnification represented by a scale bar.
representative part
Figure 7.1 has the necessary information to create a plan diagram of part of a plant stem.
of the section of the
However, it is important you create your own plan diagrams by examining prepared
stem in Figure 7.1 to
accurately record the slides, using an eyepiece graticule (page 8) to show tissues in correct proportions. Follow
distribution of the the guidance on recording observations in drawings on page 6.
tissues. Figure 7.2 has the necessary information to create a plan diagram of part of a plant leaf.
Using the However, it is important you create your own plan diagrams by examining prepared
magnification slides, using an eyepiece graticule to show tissues in correct proportions.
data given, add an
Figure 7.3 has the necessary information to create a plan diagram of part of a plant root.
appropriate scale bar
However, it is important you create your own plan diagrams by examining prepared
line to your drawing.
slides, using an eyepiece graticule to show tissues in correct proportions.
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7.2 Transport mechanisms
Learning outcomes 7
7.2.1 state that some mineral ions and organic compounds can be transported
within plants dissolved in water
7.2.2 describe the transport of water from the soil to the xylem through the:
apoplast pathway, including reference to lignin and cellulose; and the
symplast pathway, including reference to the endodermis, Casparian strip

and suberin
7.2.3 explain that transpiration involves the evaporation of water from the
internal surfaces of leaves followed by diffusion of water vapour to the
atmosphere
7.2.4 explain how hydrogen bonding of water molecules is involved with
movement of water in the xylem by cohesion-tension in transpiration pull
and by adhesion to cellulose in cell walls
7.2.5 make annotated drawings of transverse sections of leaves from
xerophytic plants to explain how they are adapted to reduce water loss by
transpiration
7.2.6 state that assimilates dissolved in water, such as sucrose and amino acids,
move from sources to sinks in phloem sieve tubes
7.2.7 explain how companion cells transfer assimilates to phloem sieve tubes,
with reference to proton pumps and cotransporter proteins
7.2.8 explain mass flow in phloem sieve tubes down a hydrostatic pressure
gradient from source to sink
Starting points
★ Movement of xylem sap and phloem sap is by mass flow. Movement in the
xylem is passive as it is driven by evaporation from the leaves; plants use
energy to move substances in the phloem.
★ Xylem sap moves in one direction: from the roots to the rest of the plant. The
phloem sap in a phloem sieve tube moves in one direction from the location
where it is made to the location where it is used or stored. At any one time
phloem sap can be moving in different directions in different sieve tubes.
The movement of water through the plant

We have seen that:
» xylem is the water conducting tissue, found in the vascular bundles of the stem and
leaves, and in the central stele of the root
» the main tap root and lateral roots grow through the soil, continuously making
contact with fresh soil
» the thin layer of dilute soil solution found around soil particles is where the plant
obtains the huge volume of water it requires
» mineral salts (ions) and organic compounds that dissolve in water can also be
absorbed from the soil solution and transported in the xylem.
Contact between root and soil is also vastly increased by structures called root hairs.
The root hairs are formed at a short distance behind the growing tip of each root. They
are extensions of individual epidermal cells and are relatively short-lived (Figure 7.8).
Elsewhere the outer cells of the root have walls that are waxy and therefore waterproof.
Consequently, it is only in the region that the root hairs occur that the root is able to
absorb water and ions.
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photomicrograph of part of TS broad bean root in
region of root hairs detail of root hairs
7
cortex
epidermal cells
(small, thin-
walled; many
bear long root-
hair extensions)
xylem and phloem tissue vacuole

nucleus cytoplasm root hair cell
cell wall
soil
particles
outer cells
of cortex soil water
soil air (dilute
solution
of ions)
▲ Figure 7.8 Root hairs – the site of absorption and uptake
Uptake of water – the roles of the root hairs

Root hairs are the point of entry of water on its passage through the green plant.
soil → root → stem → leaf → air
The very large numbers of delicate root hairs form behind each root tip (Figure 7.3).
These are in close contact with the soil solution which has a very high water potential.
(Remember, water potential, the name we give to the tendency of water molecules to
enter or leave solutions, was introduced in Topic 4, page 91.) At the same time, the cells
of the root cortex have a water potential much lower than that of the soil solution.
Water enters the root from the soil solution, passing down a water potential gradient
(Figure 7.9a).
Another process occurring in the root hairs is the active uptake of soluble ions from
the soil solution. These ions include nitrate ions, magnesium ions and several others, all
Question essential to the metabolism of the plant. Once absorbed, the ions are transported across
the cortex of the root. They converge on the central stele and there they are actively
4 What features of
secreted into the water column flowing up the xylem. The continuing movement of
root hairs facilitate
ions across the cortex of the root is partly responsible for the gradient in water potential
absorption from the
soil? between soil solution and the cells of the stele. We return to the issue of ion uptake later
in this topic.
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a)
air
From root hairs to xylem – apoplast and symplast pathways
low y
7
leaf Look at Figure 7.9b. It shows the two pathways that water can take through plant
(more
negative) tissues.
The alternative pathways of water movement shown are:
water stem » the apoplast pathway. This is the interconnected ‘free spaces’ that occur between
potential the cellulose fibres in the plant cell walls. These free spaces make up about 50 per
(y) gradient
cent of the volume of the cell wall. The apoplast also includes the water-filled spaces
of dead cells and of the xylem vessels. Note that this route entirely avoids the living

contents of cells. We shall see that most of the water passing through plant tissue
soil travels by this pathway, most of the time – a case of transport by mass flow.
» the symplast pathway. This is the living contents of cells. Water enters cells through
the cell surface membrane by osmosis and diffuses through the cytoplasm of cells
highy
(close and the cytoplasmic connections between cells (called plasmodesmata). You will
to root remember that the cells are packed with many organelles. These tend to slow the
zero)
flow of water, so this pathway is not the major one for water movement.
So, most water travels across the root via the apoplast pathway until, that is, the
endodermis is reached.
b)
water potential (y ) gradient
high y low y
apoplast pathway of water movement (= mass flow)

soil solution (through space in the wall cellulose – about 50%
of the wall volume)
cellulose cell wall
(50% free space)
cytoplasm
vacuole
root hair
cell (in
contact with nucleus
soil solution)
water moves by osmosis, symplast pathway of water movement cytoplasmic connection

into the vacuoles (through living cytoplasm by diffusion, (plasmodesmata)
including through the cytoplasmic connection
between cells)
▲ Figure 7.9 Water movement – force and pathways

a) The water potential (ψ) gradient of the whole plant
b) The water potential (ψ) gradient across cells of the root cortex
The role of the endodermis

This is a single layer of cells that surrounds the central stele of the root. These cells have
a waxy strip in their radial walls, known as the Casparian strip. The wax is so strongly
attached to the cellulose that it stops the movement of water by the apoplast pathway –
but only temporarily. All water passes into the cytoplasm of the endodermis cells and
then travels by the symplast pathway. You can see the position of the Casparian strip
Question and its effect on water movement in Figure 7.10.
5 What is the After that, water can and mostly does return to the apoplast pathway and travels the
consequence of the remaining short distance to reach the xylem vessels. This movement, too, is down a
Casparian strip for water potential gradient. However, the next steps – entry into the xylem and movement
the apoplast pathway of water up to the leaves – depend on events in the leaves. Next, we need to investigate
of water movement?
the process of loss of water vapour from the cells of the leaves.
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whole
7
plant
Water loss from xylem to
air (as vapour) in the leaf.
movement of water via

apoplast (most water
travels this way)
Heat energy from the Sun

warms the leaves, causing
spaces in evaporation of water, and
cellulose is ultimately responsible
cell walls evaporation of for drawing water up the
saturated water into plant stem (the
with water leaf air spaces transpiration stream).
water vapour waxy cuticle prevents

guard cell diffuses out of water loss through
beside open open stoma epidermal cells
water is drawn up in the
stoma
transpiration stream
endodermal cell –
Water uptake from soil solution, and its
water passes through
movement across root to xylem vessels.
cytoplasm (apoplast
pathway blocked,
Casparian strip temporarily)
wax strip in
radial wall
water apoplast pathway – water passes

movement by mass flow through free space
in between cellulose fibres of wall and
apoplast hollow (dead) xylem vessels
water
uptake
by osmosis
vacuole
xylem water
diffusion soil solution
vessel
via symplast pathway – water diffuses
endodermis symplast through living contents of cell
cytoplasm
layer around (cytoplasm and plasmodesmata)
connections
stele
between cells
(plasmodesmata)
▲ Figure 7.10 Water uptake and loss by plants
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Transpiration and the role of stomata
Transpiration is the name given to the loss of water vapour from the aerial parts of
plants. The mesophyll cells in the leaf are moist and their walls contain water between 7
all the cellulose fibres there. Consequently, there is a film of water around the outside of
the cell walls, too. So water is freely available to evaporate from the cell walls and it does
so. The air inside the leaf is usually saturated with water vapour.
Stomata are pores in the epidermis of leaves. Each stoma consists of two elongated
guard cells. These are attached to the surrounding epidermal cells and joined together
at each end but they are free to separate to form a pore between them (Figure 7.11). The

epidermal cell besides a guard cell is called a subsidiary cell.
The water vapour that accumulates in the air spaces between the mesophyll cells
diffuses out through the pores of open stomata, provided there is a concentration
gradient between the leaf spaces and the air outside the leaf. This difference in
concentration of water vapour between the leaf and the external atmosphere is highest
in hot, dry, windy weather. Transpiration is greatest in these conditions, as we shall
shortly demonstrate. The site of transpiration is shown in Figure 7.12, overleaf.
drawing of stoma in section, showing uneven thickening of walls

photomicrograph of stoma in TS (ë700) cell
mesophyll
subsidiary cell air space

associated with guard
cell (contains no
chloroplasts)
cell contents have
hardened and shrunk
during fixation of
leaf tissue
thick outer wall

of epidermis
covered by a waxy
cuticle
pore partially
open guard cell but dorsal and epidermal
has thin ventral walls are cells
lateral walls greatly thickened
with celulose
▲ Figure 7.11 The structure of stomata
Stomatal aperture and water loss – an experimental approach

Water vapour diffusing out of a leaf through open stomata can be detected by using
anhydrous copper (ii) sulfate crystals (these change from white to blue when they react
with water). The time this takes to happen will indicate the number of open stomata.
The results can be related to stomatal frequency in the same plant leaves by spreading
a film of nail varnish on the leaf surfaces. When the film has dried it can be peeled off
with fine forceps, placed on a microscope slide with a drop of water and a cover slip
added. The number of open stomata observed in the microscope field of view can be
counted. The mean of five counts for each leaf will provide a significant result.
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sunlight water drawn from xylem xylem vessels in
vessels, replacing stem (phloem
7
water lost tissue omitted)
waxy cuticle covers

epidermis – prevents
evaporation of water from
outer surfaces of plant
leaf stalk
leaf blade
high concentration
of water vapour diffusion of water
in air spaces of leaf vapour to drier pore of stomata
air outside
guard cell
air movements carry

water vapour away and
column of water drawn
maintain the gradient
Figure 7.12 The site of transpiration up the xylem by the
evaporation in the leaves
Question The transpiration stream

The water that evaporates from the walls of the mesophyll cells of the leaf is
6 Explain precisely
continuously replaced. It comes, in part, from the cell cytoplasm (the symplast pathway),
why it is that a rise
but mostly it comes from the water in the spaces in cell walls in nearby cells and
in temperature
around a green plant then from the xylem vessels in the network of vascular bundles nearby (the apoplast
normally leads to an pathway).
increase in the rate of These xylem vessels are full of water. As water leaves the xylem vessels in the leaf a
transpiration. tension is set up on the entire water column in the xylem tissue of the plant. This tension
is transmitted down the stem to the roots because of the cohesion of water molecules.
Cohesion is the force by which individual molecules stick together. Water molecules stick
together as a result of hydrogen bonding. These bonds continually break and reform
with other adjacent water molecules, but at any one moment a large number are held
together by their hydrogen bonds, and so are strongly attracted to each other.
Adhesion is the force by which individual water molecules cling to surrounding
material and surfaces. Materials with an affinity for water are described as hydrophilic
(see ‘The solvent properties of water’ on page 56). Water adheres strongly to most
surfaces and can be drawn up in long columns, through narrow tubes like the xylem
vessels of plant stems, without danger of the water column breaking (Figures 7.13 and
7.14). Compared with other liquids, water has extremely strong adhesive and cohesive
properties that prevent it breaking under tension.
Consequently, under tension the water column does not break or pull away from
the sides of the xylem vessels. The result is that water is drawn (literally pulled) up
the stem. So water flow in the xylem is always upwards. We call this flow of water
the transpiration stream and the explanation of water transport up the stem, the
cohesion–tension theory.
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heat in sunlight evaporation of water water can be drawn up to a great height without the column breaking
in the leaves off or pulling apart
7
(transpiration)

water drawn up the tree
the column of water coheres, xylem vessels run from roots to
trunk by force generated
adheres to the walls of the xylem leaves, as continuous narrow tubes
in transpiration
vessels and flows smoothly through
them (because its viscosity is low)
▲ Figure 7.14 Water is drawn up through xylem vessels
water taken from soil by root cells
▲ Figure 7.13 Water is drawn up a tree trunk
The tension on the water column in xylem is demonstrated experimentally when a

xylem vessel is pierced by a fine needle. Immediately, a bubble of air enters the column
(and will interrupt water flow). If the contents of the xylem vessel had been under
pressure, then a jet of water would have been released from the broken vessel.
Further evidence of the cohesion–tension theory comes from measurement of the
diameter of a tree trunk over a 24-hour period. In a large tree there is an easily detectable
shrinkage in the diameter of the trunk during the day. Under tension, xylem vessels get
narrower in diameter, although their collapse is prevented by the lignified thickening of
their walls. Notice that these are on the inside of the xylem vessels (Figure 7.15).
The diameter of a tree trunk recovers during the night when transpiration virtually stops and
water uptake replaces the earlier losses of water vapour from the aerial parts of the plant.
Investigating transpiration
The conditions that affect transpiration may be studied using a potometer. You will
find that these are also the conditions which effect evaporation of water from any moist
surface. They include the humidity of the air, temperature and air movements. In
Figure 7.16 the ways in which these factors may be investigated is suggested.
Actually, the potometer measures water uptake by the shoot. In the potometer the shoot
▲ Figure 7.15 Xylem vessels has an unlimited supply of water. By contrast, in the intact plant the supply of water
with internal rings of from the roots may slow down (as in drought conditions, for example), so the water
lignin thickening their supply is also a factor in the rate of transpiration in the intact plant. This point will help
lateral walls you answer Question 7.
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The factors that influence transpiration: How to investigate factor using the potometer:
7 Humidity – at low humidity more water evaporates Compare transpiration by shoot contained in polythene bag
with that by shoot in moving air
Temperature – heat energy drives evaporation from Compare transpiration at different air temperatures
surface of mesophyll cells
Air movement – wind carries away saturated air from Compare transpiration at different fan speeds
around leaves, maintaining a concentration gradient
between leaf interior and air outside stomata
Water supply – if leaves become flaccid the stomata close (Not applicable – potometer supplies unlimited water to shoot)
▲ Table 7.1 Factors that influence transpiration and how to investigate them
Question The potometer may be set up under different environmental

conditions (e.g. light v. dark; low v. high temperature; moving v. still
leafy shoot (loses air), and the rate of transpiration measured.
7 Explain the water vapour to air)
significance of the
fact that in large trees
there is an easily water drawn up the water reservoir
stem to replace the (the capillary tube is recharged
detectable shrinkage water transpired with water from here) Readings are taken of the
in the diameter of movement of the meniscus
the trunk during tap (closed) in a given time.
the daytime in hot
weather that recovers rubber
in the night. connection
capillary tube
(1mm in diameter) as water is drawn into the plant
a meniscus appears here and
Figure 7.16 Investigating moves along the capillary tube
transpiration using a
potometer
Does transpiration have a role?

We have seen that transpiration is a direct result of plant structure, plant nutrition and
the mechanism of gas exchange in leaves, rather than being a valuable process. In effect,
the living plant is a ‘wick’ that steadily dries the soil around it.
However, transpiration confers advantages, too.
» Evaporation of water from the cells of the leaf in the light has a strong cooling effect
(page 56).
» The stream of water travelling up from the roots passively carries the dissolved ions
that have been actively absorbed from the soil solution in the root hairs. These are
required in the leaves and growing points of the plant (see below).
» All the cells of a plant receive water by lateral movements of water down a water potential
gradient from xylem vessels, via pits in their walls. This allows living cells to be fully
hydrated. It is the turgor pressure of these cells that provides support to the whole leaf,
enabling the leaf blade to receive maximum exposure to light. In fact, the entire aerial
system of non-woody plants is supported by this turgor pressure (Figure 4.19, page 96).
So, transpiration does have significant roles in the life of the plant.
Xerophytes: plants of permanently dry and arid conditions
Most native plants of temperate and tropical zones and many crop plants grow best in
habitats with plenty of rain and well-drained soils. These sorts of plants are known as
mesophytes. It is the structure of these plants that has been described in this topic so
far. Typically, their leaves are exposed to moderately dry air. Much water is lost from
their leaves, particularly in drier periods. This is especially the case in the early part of
the day. Later, if excessive loss of water continues, it is prevented by the responses of the
stomata – they close (Figure 7.11). After that, the water lost can be replaced by the water
uptake that continues, day and night.
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On the other hand, some plants are well able to survive and often grow well in habitats
where water is permanently scarce. These plants are known as xerophytes. They show
features that directly or indirectly help to reduce the water loss due to transpiration to a
minimum. The adaptations they have that enable them to survive where water is short
7
are referred to as xeromorphic features. These are summarised in Table 7.2.
Structural feature Effect

Exceptionally thick cuticle to Prevents water loss through the external wall of the
leaf (and stem) epidermis epidermal cells

Layer of hairs on the epidermis Traps moist air over the leaf and reduces diffusion
Reduction in the number of Reduces the outlets through which moist air can diffuse
stomata
Stomata in pits or groves Moist air is trapped outside the stomata, reducing
Question diffusion
8 Suggest why it Leaf rolled or folded when short Reduces area from which transpiration can occur
is that, of all the of water (cells flaccid)
environmental Leaf area severely reduced – Stems take over a photosynthetic function and support
factors which affect possibly to ‘needles’ much reduced leaves
plant growth, the
Have two types of roots: Obtain water by both:
issue of water supply
is so critical. a) superficial roots exploiting overnight condensation at soil surface
b) deep and extensive roots exploiting a deep water table in the soil
▲ Table 7.2 Typical structural features of xerophytes
Sorghum, a grain plant that thrives in extremely arid conditions, shows marked adaptations
in its leaf structure and root system. Marram grass is a pioneer plant of sand dunes.
Examine Figures 7.17 and 7.18 carefully. Which of the features listed in Table 7.2 does each plant
exhibit?
part of leaf section (×150) upper epidermis
terminal
stomata
mature grains with thick waxy cuticle
flowering
ready for harvest hinge cells
inflorescence
vascular
bundle
lower epidermis
leaf with adequate water supply leaf during drought
leaf blade spread out, leaf wilts as cells

exposed to maximum become flaccid
illumination
moist air trapped on

prop roots underside of leaf –
slows water
vapour loss by
× × diffusion from
× × × × leaf via stomata
position of position of vascular

hinge cells stomata bundles
exceptionally extensive adventitious roots – tap soil to
a depth of about 1.8 m, and spread laterally 1.5 m wide
▲ Figure 7.17 Sorghum: a drought-resistant tropical plant of economic importance

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TS of leaf (×50)
7 leaf rolled, retaining moist

air over stomata,
minimising
transpiration
marram grass has the ability to grow in

the extremely arid environment of sand
dunes, accelerating the build-up of sand
lower epidermis lignified hinge cells

of leaf ground (when flaccid,
(no stomata, tissue cause leaf
very thick cells to roll up)
cuticle)
upper
epidermis
xylem
phloem
hairs – outgrowth of
epidermis – trap moist air
the more flaccid
the leaf the more
tightly rolled it becomes,
mesophyll cells with chloroplasts shutting off stomata
– stomata restricted to epidermis from outside atmosphere
above these cells
▲ Figure 7.18 Marran grass (Ammophila): a part of sand dunes
Inorganic ions and plants

‘Minerals’ are inorganic elements, some of which are needed by organisms. They include
substances like sodium chloride, in which ionic bonding occurs. In ionic bonding one
Question or more electrons is transferred completely from one atom to another, to produce a
9 Explain the stable arrangement of electrons. Ionic bonding transforms atoms into stable ions. Ionic
significance of: bonding and the formation of ions contrasts with covalent bonding, which occurs in
a root hair cells water (Figure 2.27, page 56) and in methane, for example.
being able to Living things need several different inorganic ions but only a handful are needed in
take up nitrate relatively large quantities. These are known as the major mineral elements. Major
ions from the mineral elements required by plants include anions, such as phosphate (H2PO4 −),
soil solution even nitrate (NO3−), and cations such as calcium (Ca2+), and magnesium (Mg2+).
though their
concentration in The source of mineral ions for plants is the soil solution – the layer of water that occurs
the cell is already around the individual soil particles. Here ions occur in quite low concentrations but
higher than in the plants can take them up through their root hairs. So, water uptake and the absorption of
soil mineral ions occur at the root hairs but they occur by entirely different mechanisms.
b plants often Ions are taken up selectively, by an active process, using energy from respiration. This
failing in soil that means that the ions that are useful are selected and the ions not required by the plant
is permanently are ignored. Uptake occurs by means of protein pumps (page 99) in the cell surface
waterlogged.
membrane of the root cells including root hair cells. Protein pumps are specific for
(Think about
particular ions so, if an ion is required, the particular transport protein is produced by
the importance
the cells and built into the cell membranes. If the required ion is available in the soil
of oxygen for
respiration.) solution, it can be pumped into the cell, despite there being a higher concentration in
the cell already.
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EXTENSION
Signs and symptoms of mineral deficiency
7
In the soil, the ions dissolved in the soil solution come from the mineral Question
skeleton of the soil by chemical erosion. They also come from the decay of the 10 Why and how is the
dead organic matter that is constantly being added to the soil. Among these are supply of essential
nitrate and magnesium ions, both required for particular biochemical pathways ions maintained
(Table 7.3). Consequently, plants that are deficient in these (and other) essential in the soil in
nutrients normally show characteristic signs and symptoms. Notice that the signs agriculture?

of deficiency of nitrate and magnesium ions are very similar.
Can you think why this is? Remember, the green colour of plants is due to the
presence of chlorophyll. Are nitrate and magnesium ions required for synthesis of new
chlorophyll molecules?
When deficiency symptoms appear in cultivated commercial crops, the mineral
nutrients available in the soil may be checked by chemical analysis, to confirm the
deficiency. Then, artificial fertiliser can be applied to counter the deficiency and restore
normal growth patterns.
Symptoms of deficiency Roles in metabolism

Nitrate deficiency Key ingredient in amino acid (and protein) synthesis
upper leaves light green, 1 Nitrate ions are reduced to ammonium ions:
lower leaves yellow
NO3
reduction, using
reducing power (NADH)
from respiration
NH4+
2 Ammonium ions are combined with an organic acid to form the amino acids required
for protein synthesis:
NH4+
organic acids amino acids
3 From the pool of amino acids are formed the polypeptides and proteins the cell
requires:
pool of amino acids
in cells where protein NH3
is synthesised
formation of protein
peptide bonds
amino acids
peptide bonds COOH
Nucleic acids also contain nitrogen

▲ Table 7.3 Nitrate and magnesium: symptoms of deficiency and roles in metabolism
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EXTENSION (continued)
7
Symptoms of deficiency Roles in metabolism
Magnesium deficiency Component of chlorophyll
lower leaves yellow
from margins inwards, H2C CH3
veins remain green chlorophylls a and b
H3C this is chlorophyll a;
CH3
chlorophyll b has an
N N
aldehyde group (–CHO)
Mg2+ in the place of the CH3
N N
H3C CH3 porphyrin ring

(light absorbing
O O ‘head’ of molecule)
with magnesium
O O O CH3 atom at centre
CH3 CH3 CH3
a hydrocarbon ‘tail’
CH3
Translocation
Translocation is the process by which manufactured food (sugars and amino acids –
sometimes called assimilates) are moved around the plant. This occurs in the phloem
tissue of the vascular bundles (Figure 7.1). The sugars made in the leaves in the light are
moved around the plant as sucrose. For example, young leaves export sugars to sites where
new stems, new leaves or new roots are being formed. Then, in older plants, sucrose is sent
to sites of storage, such as the cortex of roots or stems, and to seeds and fruits.
Meanwhile, nitrates are absorbed from the soil solution by the root hairs. Nitrates are one
of the raw materials used in the synthesis of amino acids and also nucleic acids. Amino
acid synthesis takes place in the roots. Amino acids are then moved to sites in the plant
where protein synthesis is occurring, such as in buds, young leaves, young roots and
developing fruits. So you can see that the contents of phloem (known as sap) may vary.
Also, it may flow in either direction in the phloem.
Phloem structure – a reminder

Phloem tissue consists of living cells – sieve tube elements and companion cells
(Figure 7.19). Both have cellulose cell walls. These walls do not become lignified.
Translocation is dependent on living cells and there is a close relationship between sieve
tube elements and their companion cells.
Sieve tubes are built from narrow, elongated cells, connected end to end to form
continuous tubes. Their touching end walls are pressed together and become perforated
by large pores which remain open. The whole structure, known as sieve plate, allows
free flow of liquid through the tube system. The cytoplasm of a mature sieve tube
element has lost its nucleus, and neither does it have many of the other organelles of a
cell. A thin layer of cytoplasm lines the walls.
At least one companion cell accompanies each sieve tube element. Sieve tube elements
and companion cells are connected by strands of cytoplasm, the plasmodesmata, that pass
through gaps in the walls. The contents of the companion cells differ from those of sieve
tube elements. They retain their nucleus and the other organelles that are common to cells
that are metabolically active – particularly mitochondria and ribosomes. We can assume
that companion cells service and maintain the sieve tube elements in various ways.
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TEM in LS companion cell and sieve tube
element in LS (high power) sieve plate in surface view
7
companion cell
sieve tube element with

companion cell end walls perforated as
cytoplasm a sieve plate

contains a nucleus,
mitochondria,
endoplasmic reticulum, lining layer of cytoplasm
Golgi apparatus with small mitochondria
sieve plate and some endoplasmic
reticulum, but without
plasmodesmata – nucleus, ribosomes or
cytoplasmic Golgi apparatus
phloem tissue in TS (low power) connections with
sieve tube elements, sieve tube
each with a cell cytoplasm
companion cell
sieve plate
▲ Figure 7.19 The fine structure of phloem
Questions Phloem transport

11 What does the Phloem transport occurs by mass flow but the pressure difference that drives it is
presence of a produced by a different mechanism from that in xylem transport. Most significantly,
large number of translocation requires living cells (Figure 7.20, overleaf). Cell respiration is the process
mitochondria in the by which energy is transferred to drive metabolic reactions and processes. Much of the
companion cells respiration occurs in the mitochondria. ATP is the molecule produced in mitochondria to
suggest to you about transfer energy. We shall see that ATP is involved in the mechanism of phloem transport.
their role in the Translocation can be illustrated by the movement of sugar from the leaves. The story
movement of sap in
starts at the point where sugars are made and accumulate within the mesophyll in the
the phloem?
leaf. This is the source area.
12 Examine Figure 7.20
carefully. Sugars are loaded into the phloem sieve tubes through transfer cells (Figure 7.21,
a What sequence overleaf). From here, sucrose is pumped into the companion cells by the combined
of events would action of primary and secondary pumps. These pumps are special proteins in the
you anticipate in cell surface membrane. The primary pumps remove hydrogen ions (protons) from the
a leaf stalk as the cytoplasm of the companion cell, so setting up a gradient in concentration of hydrogen
content of a water- ions between the exterior and interior of the companion cell. This movement requires
jacket is raised to ATP. Hydrogen ions then flow back into the companion cell down their concentration
50°C? gradient. This occurs at specific sites called secondary pumps where their flow is linked
b How would you to the transport of sucrose molecules in the same direction.
expect the phloem As sucrose solution accumulates in the companion cells it moves on by diffusion into the
sap sampled from sieve tubes, passing along the plasmodesmata (Figure 7.19). The accumulation of sugar
a sieve tube near
in the phloem tissue lowers the water potential and water follows the sucrose, diffusing
leaves in the light
down a water potential gradient. This creates a high hydrostatic pressure in the sieve
and at the base of
tubes of the source area.
the same stem to
differ? Meanwhile, in living cells elsewhere in the plant – often, but not necessarily in the roots,
sucrose may be converted into insoluble starch deposits. This is a sink area. As sucrose
flows out of the sieve tubes here, the water potential is raised. Water then diffuses
out down a water potential gradient and the hydrostatic pressure is lowered. These
processes create the difference in hydrostatic pressures in the source and sink areas that
drives mass flow in the phloem.
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Figure 7.20 condition water at different (a) at 50°C, translocation of sugar
That translocation requires living
Experiment of leaf blade temperatures from the leaf blade stopped – this
cells is shown by investigation of
7 to show that
translocation
the effect of temperature on
phloem transport
monitored (3, 20 and 50°C)
passed through
is above the thermal death point of
cytoplasm
water jacket
requires
conclusion: living cells are
living cells
Note: in neither experiment did the essential for translocation
leaf blade wilt – xylem transport is
not heat sensitive at this range of (b) at 3°C, compared with 20°C
temperatures (because xylem vessels translocation of sugar from leaf
are dead, empty tubes) blade was reduced by almost 10%
of leaf dry weight over a given time
water
jacket
output conclusion: rate of metabolic
activity of phloem cells affects
rate of translocation
Figure 7.21 TEM of a leaf vein showing sieve tube elements, transfer cells, xylem vesssels and mesophyll cells (x1500)
Transfer cells and
the loading of sieve phloem
tubes xylem vessels
companion cell
with thickened,
phloem lignified walls
sieve tubes and permeable
pit areas – here
transfer cells water can pass
– here many into surrounding
cell wall in-growths cells
greatly increase part of a
the surface area mesophyll cell
of the cell surface with large central
membrane. In these vacuole and with
membranes are chloroplasts present
the protein pumps in the lining cytoplasm
that transfer sucrose
into sieve tubes
leaf in cross section upper epidermis
palisade mesophyll
xylem vessels
position of transfer cells phloem sieve tube
spongy mesophyll elements
lower epidermis
membrane of
transfer cells around phloem sieve tubes proton pump transfer cell
(primary pump) ADP
H+ H+
plasmodesmata driven by ATP
mesohpyll cell membrane pump ATP Ai
(secondary pump) – H+ H+
xylem vessel here proton flow sucrose
transfer cell
is linked to sucrose
sieve tube transport transfer of sugar, driven
by a flow of protons down
their concentration gradient
The pressure flow hypothesis

The principle of the pressure flow hypothesis is that the sugar solution flows down a
hydrostatic pressure gradient. There is a high hydrostatic pressure in sieve elements near
mesophyll cells in the light (source area) but low hydrostatic pressure in elements near
starch storage cells of the stem or root (sink area). Mass flow is illustrated in Figure 7.22
and the annotations explain the steps.
In this hypothesis, the role of the companion cells (living cells, with a full range of
organelles in the cytoplasm) is to maintain conditions in the sieve tube elements
favourable to mass flow of solutes. Companion cells use metabolic energy (ATP) to do this.
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Question For Against
13 What conditions
maintain
The contents of the sieve tubes are under
pressure and sugar solution exudes if
Phloem tissue carries manufactured food
to various destinations (in different sieve 7
a the high water phloem is cut. tubes), rather than to the greatest sink.
potential of the Appropriate gradients between ‘source’ and Sieve plates are a barrier to mass flow and
cell of the root ‘sink’ tissue do exist. might be expected to have been ‘lost’ in
cortex the course of evolution if mass flow is the
b the low water mechanism of transport.
potential of the ▲ Table 7.4 Evidence for the pressure flow hypothesis

mesophyll cells of
a green leaf?
model demonstrating pressure flow

concentrated sugar solution flow of solution water or very dilute
(A = mesophyll cell, B = starch storage cell) (low water potential) in (= phloem) solution of ions (high
partially permeable water potential) in
reservoir (non-elastic) partially permeable
reservoir (non-elastic)
In this model, the pressure flow of

solution would continue until the
concentration in A and B is
the same.
water A B water
net water entry water flow by

by osmosis hydrostatic pressure
flow of water
(= xylem)
pressure flow in the plant sunlight
source cell, e.g. mesophyll cell

of leaf where sugar is formed
(= A)
chloroplast (site of
sugar manufacture by
photosynthesis)
water loss by evaporation
high hydrostatic pressure
due to dissolved sugar
In the plant, a concentration difference between

A and B is maintained by conversion of sugar to sugar loaded
starch in cell B, while light causes production of into sieve
sugar by photosynthesis in A. tube
mass flow
along sieve tube
transpiration stream element from high
to low
hydrostatic
pressure zone
xylem
low hydrostatic pressure

here because sugar is
converted to insoluble
starch
water uptake in root hair

sink cell, e.g. starch
storage cell (= B)
▲ Figure 7.22 The pressure flow hypothesis of phloem transport

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SUMMARY
7 » Internal transport within plants occurs by mass surfaces, is responsible for the cohesive and
flow but there is no pumping organ. Two separate adhesive properties of water, and makes possible
tissues are involved in transport. Water and ions the upward transport of water in the xylem by
travel in the xylem, a system of vessels connected cohesion–tension.
end to end to form non-living tubes. Manufactured » Transport of manufactured food in the phloem is
foods are carried in a living tissue, the phloem, by active transport requiring living phloem cells.
consisting of sieve tubes and companion cells. The According to the mass flow hypothesis, solutes
xylem and phloem make up the vascular tissue flow through the phloem from a region of high
that branches throughout the plant body and serves hydrostatic pressure to a region of low hydrostatic
roots, stems, leaves and growing points (buds). pressure. Hydrostatic pressure is high in cells
» Water moves from the soil to the aerial system where sugar is formed, the source area, but low in
by a gradient in water potential. Water is drawn sink areas, where sugar is converted to starch.
up the stem by a force generated in the leaves by » Plants that survive permanently arid conditions
the evaporation of water vapour from the aerial (xerophytes), including the crop plant Sorghum and
system (transpiration). the sand-dune plant Marram grass, have leaves
» Hydrogen bonding between water molecules, adapted to reduce water loss by transpiration.
and between these molecules and hydrophilic

1 Sugar molecules enter cells through transport proteins.
a Explain why transport proteins are required for the movement of sugar
molecules, such as glucose and fructose, into cells. [2]
Some plant cells convert fructose and glucose into sucrose for transport from
sources to sinks.
Sucrose is moved into phloem sieve tubes as shown in Fig. 1.1.
H+
H+ H+ H+
Y H+ H+ H+ X
cell surface
membrane of
companion cell
ATP ADP + Pi
H+ H+
cell walI
mesophyll
cell
companion
cell
sieve tube not to scale

element
▲ Fig. 1.1
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482876_07_Biology_142-165.indd 164 22/02/20 11:42 AM

b Use the information in Fig. 1.1 to explain how sucrose:
» moves into the companion cell
» moves from the companion cell into the sieve tube element. [5] 7
c Sucrose travels in phloem sieve tubes to sinks.
State two examples of sinks. [1]
[Total: 8]
2 a Draw and annotate a diagram of a potometer in use in the measurement of
transpiration. [8]

b Name three external factors that may influence the rate of transpiration in
a plant in the light and explain why they have an effect on the rate of loss
of water vapour. [6]
c What is a xerophyte? [1]
d Tabulate the chief xeromorphic features that Sorghum exhibits and explain
how and why they are effective. [5]
[Total: 20]
3 Fig. 3.1 is a diagram of a section through part of a young root.
film of water X
soil particle
cortex
▲ Fig. 3.1
a Describe the pathways by which water passes from the soil to the cells of the
cortex shown in Fig. 3.1. [4]
b There is a greater density of mitochondria in the cytoplasm of cell X than in the
cytoplasm of a cell of the cortex.
Suggest why this is so. [1]
[Total: 5]
(Cambridge International AS and A Level Biology 9700 Paper 22 Q4 Feb/Mar 2018)
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AS LEVEL
As animals become larger, Learning outcomes

more complex and more
active, transport systems
become essential to supply 8.1.1 state that the mammalian circulatory system is a closed double
nutrients to, and remove circulation consisting of a heart, blood and blood vessels including
waste from, individual cells. arteries, arterioles, capillaries, venules and veins
Mammals are far more active 8.1.2 describe the functions of the main blood vessels of the pulmonary and
than plants and require systemic circulations, limited to pulmonary artery, pulmonary vein, aorta
much greater supplies of and vena cava
oxygen. This is transported
by haemoglobin inside red
8.1.3 recognise arteries, veins and capillaries from microscope slides,
blood cells. photomicrographs and electron micrographs and make plan diagrams
showing the structure of arteries and veins in transverse section (TS) and
longitudinal section (LS)
8.1.4 explain how the structure of muscular arteries, elastic arteries, veins and
capillaries are each related to their functions
8.1.5 recognise and draw red blood cells, monocytes, neutrophils and
lymphocytes from microscope slides, photomicrographs and electron
micrographs
8.1.6 state that water is the main component of blood and tissue fluid and relate
the properties of water to its role in transport in mammals, limited to
solvent action and high specific heat capacity
8.1.7 state the functions of tissue fluid and describe the formation of tissue fluid
in a capillary network
Starting point
★ The mammalian circulatory system consists of a pump, many blood vessels and
blood, which is a suspension of red blood cells and white blood cells in plasma.
8.1 The circulatory system

Efficient internal transport in animals
The cells of organisms need a constant supply of water and organic nutrients such
as glucose and amino acids; most need oxygen, and the waste products of cellular
metabolism have to be removed. Larger animals have evolved a blood circulatory
system for efficient internal transport. This links the parts of the body and makes these
resources available where they are required.
Mammals have a closed circulation in which blood is pumped by a powerful, muscular
heart and circulated in a continuous system of tubes – the arteries, veins and capillaries –
under pressure. The heart has four chambers and is divided into right and left sides.
Blood flows from the right side of the heart to the lungs, then back to the left side of the
heart. From here it is pumped around the rest of the body and back to the right side of
the heart. As the blood passes twice through the heart in every single circulation of the
body this is called a double circulation. The circulatory system of mammals is shown
in Figure 8.1, alongside alternative systems.
Look at these systems carefully.
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open circulation of insects closed circulation systems double circulation of mammals
blood is pumped forwards in the tubular heart, and then blood passes twice through the
passes in the sinuses (open spaces) between the organs
dorsal blood vessel
heart in each complete circulation
8
wings
is a tubular heart
valves allow blood to pulmonary circulation
enter, and to be pumped single circulation of fish (to lungs)
forwards blood passes once through
the heart in each complete
circulation four-chambered
heart
blood pumped then on to the

to the gills first rest of the body systemic circulation
perforated membranes (to body tissues)
aid circulation in the
sinuses
limbs
two-chambered heart
▲ Figure 8.1 Open and closed circulations
Looking at these other systems helps us to understand the features of the mammalian
Question circulation. It becomes clear that the major advantages of the mammalian circulation are:
1 In an open » simultaneous high pressure delivery of oxygenated blood to all regions of the body
circulation there is » oxygenated blood reaches the respiring tissues, undiluted by deoxygenated blood.
‘little control over
circulation’. Suggest Blood circulation in mammals
what this means.
Mammals have a closed circulation system in which blood is pumped by a powerful,
muscular heart and circulated under pressure in a continuous system of tubes – the
arteries, arterioles, capillaries, venules and veins. The heart has four chambers, and
is divided into right and left sides. This is shown in Figure 8.2 overleaf, which shows the
layout of the human blood circulation.
EXTENSION
The hepatic portal vein
The blood supply to the liver is via the hepatic artery but the liver also receives blood
directly from the small intestine, via a vein called the hepatic portal vein. This
brings much of the products of digestion, after they have been absorbed into the
capillaries of the villi in the small intestine.
Pulmonary circulation
Looking at Figure 8.2, notice that blood is pumped from the right side of the heart to
the lungs via the pulmonary artery. From the lungs, blood returns to the left side of
the heart via the pulmonary vein. This part of the system is called the pulmonary
circulation. The sequence in the circulation is:
pulmonary artery S arteriole S capillary S venule S vein S pulmonary vein
Systemic circulation
From the left side of the heart, blood is pumped around the rest of the body via the
aorta (the main artery) before returning to the right side of the heart via the vena
cava (the main vein). This is called the systemic circulation. The sequence in the
circulation is:
aorta S artery S arteriole S capillary S venule S vein S vena cava
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The position of the major vessels The layout of the blood circulation
8
head
upper limbs
lungs
pulmonary artery pulmonary vein
pulmonary
circulation
systemic
aorta circulation
vena cava
right left
atrium atrium
right left
ventricle ventricle
heart
liver
stomach/intestines
renal vein renal artery
kidneys
gonads (ovaries, testes)

the circulatory system as shown here is simplified, e.g. limbs,
lungs, kidneys and gonads are paired structures in the body
lower limbs
▲ Figure 8.2 The human blood circulation
You can see that blood passes twice through the heart in every single circulation of the
body. This arrangement is a called a double circulation. This means there is no mixing
of oxygenated and deoxygenated blood in the heart, so the blood circulating around the
body has a higher concentration of oxygen than would otherwise be possible.
Arteries, veins and capillaries

There are three types of vessel in the circulation system, each with different roles.
» Arteries carry blood away from the heart.
» Veins carry blood back to the heart.
» Capillaries are fine networks of tiny tubes linking arteries and veins.
In Figure 8.2 you can see how the main arteries and veins serve the organs of the body.
(Notice that arteries and veins are often named after the organs they serve.)
For example, in the systemic circulation, each organ is supplied with blood by a separate
artery that branches from the main aorta. Inside organs, the artery branches into
numerous arterioles (smaller arteries). The smallest of these arterioles supply numerous
and very extensive capillary networks. These capillaries then drain into venules
(smaller veins) and these venules join to form veins. Finally, the veins join the vena
cava carrying blood back to the right side of the heart.
The structure of arteries, capillaries and veins

Blood leaving the heart is under very high pressure and travels in waves or pulses
following each heart beat. By the time the blood has reached the capillaries it is under
very much lower pressure, without a pulse. These differences in blood pressure account
for the differences in the wall structure of arteries and veins. There are many subtle
changes on the way between a main artery and the corresponding vein.
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artery outer layer (tunica vein
externa) of elastic fibres
and collagen
middle layer (tunica media) 8
of elastic fibres, collagen
and smooth
muscle fibres
the hollow centre of
a tube is the lumen
endothelium
(inner lining) of squamous

epithelium – single layer
of cells with smooth inner
surface
capillary wall (enlarged)

TS artery and vein, LP (320) – in sectioned material (as here), substances leave (and
veins are more likely to appear squashed, whereas arteries enter) capillaries
through the walls
are circular in section
basement endothelial cells

▲ Figure 8.3 The structure of the wall of arteries, veins membrane
and capillaries
Arteries and veins have three distinct layers to their walls (Figure 8.3 and Table 8.1).
Both arteries and veins have strong, elastic walls but the walls of the arteries are very
much thicker and stronger than those of the veins. The strength of the walls comes from
a combination of collagen and elastic fibres. Their elasticity is due to the elastic fibres and
to the involuntary (smooth) muscle fibres.
Capillaries have an altogether different structure – they consist of a single layer of cells
and they are tiny in cross-section when compared with the main arteries and veins.
The importance of elastic arteries

As the ventricles of the heart contract, blood is forced into arteries at very high pressure
but the ventricles must then relax to refill with blood. The result of this could be that
the blood would flow in a stop–start fashion. Obviously, this would be very inefficient.
However, elastic fibres and smooth muscle in the walls of arteries are stretched when the
blood is at high pressure. Therefore, some of the energy in the blood is stored as
blood flow back
to the heart potential energy in the elastic walls of the arteries. When the pressure of the blood
valve is opened by falls, this stored energy is used to maintain the flow until the ventricles contract
blood pressure again. In this way the pressure fluctuations of the blood are smoothed out to give a
from behind more continuous flow. This is known as elastic recoil of arteries.
The importance of valves in veins

Having squeezed through the capillary network, blood in veins is at a low pressure,
pressure from movements
of the surrounding tissues, yet still needs to be returned to the heart. For example, low-pressure blood in veins
including contractions of in your feet has to be pumped a vertical height of about a metre to reach the heart.
the muscles, which Veins have valves at intervals, which prevent the backflow of blood (Figure 8.4).
compresses the vein
These valves also mean that as surrounding muscles contract and press against the
blood flow veins, they force the blood from one valve to the next, so helping the return flow.
reversed
Observing and drawing the structure of arteries, veins and capillaries
valve is closed by
blood pressure You need to observe and draw the structure of arteries, veins and capillaries,
from in front using prepared slides and a light microscope under medium and high power
▲ Figure 8.4 The valves in veins magnification, so that you will be able to recognise them.
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Artery Capillary Vein
8 Outer layer (tunica externa) of elastic fibres and collagen

Middle layer (tunica media) of elastic fibres, collagen and
Present – thick layer
Present – thick layer
Absent
Absent
Present – thin layer
Present – thin layer
involuntary (smooth) muscle fibres
Endothelium (inner lining) of squamous epithelium – a Present Present Present
single layer of cells fitting together like jigsaw pieces,
with a smooth inner surface that minimises friction
Valves Absent Absent Present
▲ Table 8.1 Differences between arteries, capillaries and veins

Now look carefully at the photomicrograph of an artery and vein in section and the details the
wall structure of these three vessels (Figure 8.3).
If you examine a prepared slide of an artery and vein under the high power of a
microscope you may see the layers of the walls in detail and you may be able to make
out the muscle fibres. Because of the low pressure in veins there is a possibility of back-
flow here. Veins have valves at intervals that prevent this (Figure 8.4).
We have noted that, as blood is transported around the body the pressure of blood
progressively falls. This fact and the roles of the arteries, capillaries and veins are
reflected in specific changes in their structure (Table 8.2).
Component and role Structure in relation to function
Arteries: have the thickest and strongest walls; the tunica media is the thickest layer.
Aorta: receives blood pumped from » The walls stretch to accommodate the huge surge of blood when the
the heart in a ‘pulse’ (pressure about ventricles contract. The elastic and collagen fibres of the tunica externa
120 mmHg). prevent rupture as blood surges from the heart.
Main arteries: distribute blood under » The high proportion of elastic fibres are first stretched and then recoil,
high pressure to regions of the body. keeping the blood flowing and propelling it forwards after each pulse.
» Arteries become wider, so lowering the » With increasing distance from the heart the tunica media progressively contains
pressure. more smooth muscle fibres and fewer elastic fibres. By varying the constriction
» Supply the smaller branch arteries that and dilation of the arteries, blood flow is maintained. Muscle fibres stretch
distribute blood to the main organs. and recoil, tending to even out the pressure but a pulse can still be detected.
Arterioles: deliver blood to the tissues. » Small muscular arteries; the walls have a high proportion of smooth muscle fibres.
» They regulate blood flow from the arteries into the capillaries through
vasoconstriction (when the arterioles contract and narrow to reduce blood
flow) and vasodilation (when the arterioles relax and widen to allow greater
blood flow).
Capillaries
Capillaries: serve the tissues and cells » Narrow tubes, about the diameter of a single red blood cell (about 7 μm),
of the body. The blood is under lower reduce the flow rate to increase exchange between blood and tissue.
pressure (about 35 mmHg). » Thin walls of a single layer of endothelial cells.
» The walls have gaps between cells sufficient to allow some components of
the blood to escape and contribute to tissue fluid (page 174).
Veins: have thin walls; the tunica externa is the thickest layer.
Venules: collect blood from the tissues. » The walls consist of endothelium and a very thin tunica media of a few
They are formed by the union of several scattered smooth muscle fibres.
capillaries (pressure about 15 mmHg).
Veins: receive blood from the tissues under » The tunica externa, containing elastic and collagen fibres, is present.
low pressure (pressure about 5 mmHg). » The tunica media contains a few elastic fibres and muscle fibres.
» The veins become wider, so lowering » The presence of valves prevents the back-flow of blood.
pressure and increasing the flow rate.
▲ Table 8.2 The changing structure of blood vessels in relation to function
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Questions 2 List the differences between the pulmonary circulation and the systemic circulation
of blood.
3 The graph in Figure 8.5 shows the changing blood velocity, blood pressure
8
and cross-sectional area of the vessels as blood circulates in the body. Use the
information in the graph and in Table 8.1 where appropriate to answer the questions
below.
sys
velocity of blood tol
e
dia

sto
le
blood pressure sys

tol
e
dia
sto
le
total cross-
sectional area
of vessels
arteries arterioles capillaries venules veins
▲ Figure 8.5 The changing blood velocity, blood pressure and cross-sectional area of
the vessels as blood circulates in the body
a Comment on the velocity and pressure of the blood as it enters the aorta
compared with when it is about to re-enter the heart.
b What aspects of the structure of the walls of arteries may be said to be in
response to the condition of blood flow through them?
c What factors may cause the velocity of blood flow to be at the level it is in the
capillaries and why is this advantageous?
Blood – the transport medium

Blood is a special tissue of several different types of cell suspended in a liquid medium
called plasma (Figure 8.6). Plasma is a straw-coloured, very slightly alkaline liquid
consisting mainly of water. The high specific heat capacity of water (meaning that a lot
of energy is required to change its temperature, see page 55) helps with maintaining a
stable body temperature. Water is also a powerful solvent for polar substances, which
makes plasma the medium for the continual exchange of substances by cells and tissues
Question throughout the body.
4 Assuming the body Dissolved in the plasma are nutrients in transit from the gut or liver to all the cells.
contains 5 litres of Excretory products are also transported in solution, mainly urea from the liver to the
blood, that there are kidneys. So too are hormones, from the ductless (endocrine glands), where they are
5 million (5 3 106) formed and released, to the tissues and organs.
red blood cells per The plasma also contains dissolved proteins. The principle blood protein is albumin,
mm3 and that a red which has the role of regulating the water potential of the blood. The presence of
blood cell lasts for dissolved albumin stops too much water leaving at the capillaries by osmosis and also
120 days, how many
helps in the return of fluids (Figure 8.8, page 175). Albumin and other proteins also
red blood cells must
assist in the transport of lipids and iron in the plasma. Other blood proteins present are
be replaced per day?
antibodies (page 227) and components of the blood clotting mechanism.
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a) blood plasma
8 plasma (55%)
cells (45%) water (90%)
dissolved substances (10%)

• proteins (7%)
• salts (1%)
• lipids (2%)
red blood cells white blood cells (leucocytes) platelets

(erythrocytes) (many have unusually shaped nuclei) (7000/mm3) (250 000/mm3)

(5 million/mm3)
lymphocytes
(form antibodies) monocytes neutrophils
phagocytes
(engulf bacteria)
b) Suspended in the plasma are the blood cells. The

majority of these are red blood cells (erythrocytes)
– about 5 million in every cubic millimetre of
blood. The red blood cells are formed in the bone
marrow tissue. Initially each red blood cell has a
nucleus but early in development the nucleus is
lost and these tiny cells (7 µm in diameter) adopt
the shape of a biconcave disc. Mitochondria and
endoplasmic reticulum are also lost and a great
deal of a protein, haemoglobin, takes their place,
together with the enzyme carbonic anhydrase.
The role of mature red blood cells is exclusively
the transport of respiratory gases in the blood. The
lifespan of a working red blood cell is only about
120 days, after which they are broken down and
▲ Figure 8.6 a) The composition of the blood; b) Blood smear replaced. Most of their components are retrieved
stained to show the few white blood cells present and reused.
Also present are some white blood cells (leucocytes) – about 7000 per cubic
millimetre of blood. These also originate in the bone marrow but they retain their
nucleus. In the growth and development stage, white blood cells may migrate to the
thymus gland, lymph nodes or the skin. The white blood cells do not necessarily
function in the bloodstream but all use the blood circulation as a means of reaching
specific body organs or tissues. Many leave the bloodstream by migrating between
the cells of the capillary wall. There are several different types of white blood cells,
all of which play a part in the body’s defences (Topic 11) and are mostly relatively
short-lived cells. The white blood cells that are particularly important are:
» lymphocytes – these form antibodies
» phagocytes – these ingest bacteria or cell fragments.
The blood also contains platelets, best described as cell fragments. These are tiny
packages of cytoplasm containing vesicles of substances that, when released, have a role
in the blood clotting mechanism.
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Observing and drawing the structure of red blood cells, monocytes,
neutrophyls and lymphocytes
You need to observe and draw the structure of red cells, monocytes, neutrophyls and
8
lymphocytes, using photomicrographs and prepared slides and a light microscope under
medium and high power magnification, so that you will be able to recognise them.
Component Role
Plasma Transport of:
» nutrients from the gut or liver to all the cells

» excretory products such as urea from the liver to the kidneys
» hormones from the endocrine glands to all tissues and organs
» dissolved proteins which have roles including regulating the
osmotic concentration (water potential) of the blood
» dissolved proteins that are antibodies
Heat distribution to all tissues
Red blood cells Transport of:
(erythrocytes) » oxygen from the lungs to respiring cells
» carbon dioxide from respiring cells to the lungs (also carried in
plasma)
White blood cells Lymphocytes: major roles in the immune system, including forming
(leucocytes) antibodies (Topic 7)
Phagocytes: ingest bacteria and cell fragments
Platelets Part of the blood clotting mechanism
▲ Table 8.3 A summary of the roles of blood components
The roles of the blood circulation system

The blood circulation has a role in the body’s defence against diseases (Topic 11), in
internal communications and in the maintenance of a constant internal
environment (Topic 14), as well as being the transport system of the body. It is the
transport roles of the blood circulation (Table 8.4), a key feature of which is the
formation and fate of tissue fluid, that we consider next.
Function in organism Transport role of circulation

Tissue respiration Transport of oxygen to all tissues and carbon dioxide
back to the lungs
Hydration Transport of water to all the tissues
Nutrition Transport of nutrients (sugars, amino acids, lipids,
vitamins) and inorganic ions to all cells
Excretion Transport of waste products of metabolism to kidneys,
lungs and sweat glands
Temperature regulation Distribution of heat
Development and coordination Transport of hormones from endocrine glands to target
organs
▲ Table 8.4 Transport roles of the blood circulation
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Exchange in the tissues and the formation of tissue fluid
8 The blood circulation delivers essential resources (nutrients and oxygen, for example) to
the tissues of the body. This occurs as the blood flows through the capillaries, between
the cells of the body (Figure 8.7). There are tiny gaps in the capillary walls, found to
vary in size in different parts of the body. Through these gaps passes a watery liquid,
very similar in composition to plasma. This is tissue fluid. However, red blood cells,
platelets and most blood proteins are not present in tissue fluid, instead these are
retained in the capillaries. Tissue fluid bathes the living cells of the body. Nutrients
are supplied from this fluid and carbon dioxide and waste products of metabolism are
carried away by it.

capillary wall (enlarged) substances leave (and enter)
capillaries through the walls
cells take in nutrients cells give out waste

(e.g. oxygen, glucose, products (e.g. carbon
amino acids, fatty acids, dioxide, unwanted
vitamins, ions) metabolites, excess ions) vein
tissue fluid formed venule

from blood plasma
basement endothelial cells cells
membrane semilunar valve
bathed
in tissue
fluid
blood flow
back to the
heart
blood flow arteriole

from the
heart tissue fluid forced into
lymph capillaries and
(blood) capillaries by
movements of
pre-capillary sphincter surrounding tissues
(when this contracts and by pressure
most of the blood is
lymph
sent along the by-pass
artery capillary
vessel)
capillary
network
by-pass vessel semilunar valve
The role of the by-pass vessel

Which tissues of the body are being served by the blood circulation is regulated. When tiny pre-capillary sphincter muscles are
contracted, blood flow to that capillary bed is restricted to a minimum. Most blood is then diverted through by-pass vessels – it is
shunted to other tissues and organs in the body.
▲ Figure 8.7 Exchange between blood and cells via tissue fluid
Given the quantity of dissolved solutes in the plasma (including and especially all the
blood plasma proteins), we would expect the water potential of the blood to limit the
loss of water by osmosis. In fact, we might expect water to be passing back into the
capillaries from the tissue fluid, due to osmosis. However, the force applied to the blood
by the heart creates enough hydrostatic pressure to overcome osmotic water uptake, at
least at the arteriole end of the capillary bed. Here the blood pressure is significantly
higher than at the venule ends. Then, as the blood flows through the capillary bed there
is progressive loss of water and of hydrostatic pressure, too. As a result, much of the
tissue fluid is able to eventually return to the plasma – about 90 per cent returns by this
route (Figure 8.8).
So, further along the capillary bed there is a net inflow of tissue fluid to the capillary.
However, not all tissue fluid is returned to the blood circulation by this route – some
enters the lymph capillaries (Figure 8.9). Lymph is the tissue fluid that drains into the
lymphatic vessels, rather than directly back into a blood capillary.
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Blood proteins, particularly the albumins, cannot escape; they maintain the water potential of
the plasma, preventing excess loss of water and assisting the return of fluid to the capillaries.
arteriole end venule end
8
blood in
capillary
ultrafiltration diffusion gradient osmotic osmotic diffusion gradient hydrostatic

of water and small (oxygen and nutrients movement movement (waste metabolites) pressure

molecules (oxygen, required by respiring of water of water reduced
glucose, amino cells)
acids) due to
hydrostatic pressure
net outflow net inflow

tissue fluid
▲ Figure 8.8 Forces for exchange in capillaries
lymph drains into the blood circulation via

ducts that join the veins in the neck a lymph node in section
fixed macrophages
engulf bacteria, debris
this duct drains and toxins by phagocytosis
the right side of
this duct drains
the head and thorax
the remainder certain cells of the immune system
and the right arm
of the body (lymphocytes and plasma cells)
are made here
lymphatic
the lymphatic circulation

lymph the flow of lymph is propelled by
lymph nodes contraction of smooth muscle
veins nodes fibres in the walls of the lymphatics
returning and by the movement and
blood to lymph ducts pressures of the surrounding tissues
(lymphatics) – lymph Backflow is prevented by valves
the heart 10% of
lymph capillary
tissue fluid
lacteals of the small capillaries body tissues –
becomes
intestine (site drain into here metabolites are
lymph
of absorption these delivered, respiratory gases
of products of 90% of tissue are exchanged and
lipid digestion) fluid is returned waste products are
drain into the to the capillaries removed by the tissue fluid
lymphatic heart
system blood artery
capillaries
groups of vein
lymph nodes
▲ Figure 8.9 The layout and role of the lymphatic system
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Question Molecules too large to enter capillaries are removed from the tissues via the lymph
system. There are tiny valves in the walls of the lymph capillaries that permit this. The
8 5 a What components
of the blood are
network of lymph capillaries drains into larger lymph ducts (known as lymphatics).
Then, lymph is moved along the lymphatics by contractions of smooth muscles in their
not found in tissue walls and by compression from body movements. Back-flow is prevented by valves, as it
fluid? is in the veins.
b Construct a table
Lymph finally drains back into the blood circulation in veins close to the heart. At
to summarise
intervals along the way there are lymph nodes present in the lymphatics. Lymph
the differences
passes through these nodes before it is returned to the blood circulation. In the nodes
between tissue
fluid and lymph. phagocytic macrophages engulf bacteria and any cell detritus present. Also the nodes
are a site where certain cells of the immune system are found. We return to this issue
in Topic 11.
EXTENSION
Oedema – fluid retention in the body
If the volume of fluid that filters out exceeds that which is re-absorbed, the result
is a greatly increased volume of tissue fluid. The result is swelling of the tissues
(oedema). This condition normally arises due either to increased blood pressure or
increased permeability of capillary walls. However, a diet that is chronically deficient
in protein may trigger the disease of kwashiorkor, a symptom of which includes
oedema.
Can you see why? The answer lies in the importance of blood proteins in maintaining the
osmotic potential of the blood (see Figure 8.8).
8.2 Transport of oxygen and carbon dioxide

Learning outcomes
8.2.1 describe the role of red blood cells in transporting oxygen and
carbon dioxide with reference to the roles of: haemoglobin, carbonic
anhydrase, the formation of haemoglobinic acid and the formation of
carbaminohaemoglobin
8.2.2 describe the chloride shift and explain the importance of the chloride shift
8.2.3 describe the role of plasma in the transport of carbon dioxide
8.2.4 describe and explain the oxygen dissociation curve of adult haemoglobin
8.2.5 explain the importance of the oxygen dissociation curve at partial
pressures of oxygen in the lungs and in respiring tissues
8.2.6 describe the Bohr shift and explain the importance of the Bohr shift
Starting points
★ Once gas exchange has taken place it is vital that the oxygen is delivered
and carbon dioxide removed from all the tissues of the body in an equally
efficient manner.
★ This requires a specialised system for loading and unloading the gases in
the blood.
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Haemoglobin
A single red blood cell contains about 280 million molecules of haemoglobin. Mammalian
erythrocytes have no nucleus but their cytoplasm is rich in haemoglobin. They are 8
biconcave (disc-shaped) and have typical cell surface membranes, which gives them a
large, thin surface area ideal for transfer of gases by diffusion and the maximum volume of
haemoglobin. We have seen that each haemoglobin molecule is built of four, interlocking
subunits composed of a large, globular protein with a non-protein haem group, containing
iron, attached (Figure 2.24, page 52).
8.2 Transport of oxygen and carbon dioxide

Partial pressures
Air is a mixture of several different gases. The total pressure of the air is made up of the
sum of the pressures of the individual gases. So, if atmospheric pressure is, say 100 kPa,
this does not mean that all the gases within it are at a pressure of 100 kPa. To calculate the
individual pressures of the gases in the mixture we simply use their relative abundance
in the mixture. Therefore, if air is 21 per cent oxygen, its partial pressure would be
21 per cent of 100 = pO2 = 21 kPa. To show this is part of a mixture we use the term
partial pressure ( p). So, in this case, the partial pressure of the oxygen is 21 kPa. We will
often refer to partial pressures in gas exchange because there is almost always a mixture of
gases involved and we wish to consider each one individually.
Oxygen
At the concentration of oxygen that occurs in our lungs, one molecule of oxygen will
combine with each haem group. This means each haemoglobin molecule is able to
transport four molecules of oxygen.
haemoglobin 1 oxygen S oxyhaemoglobin

Hb 4O2 HbO8
Figure 8.10 shows the relationship between haemoglobin and oxygen as the
concentration of oxygen around the haemoglobin molecule changes. (Oxygen
concentration is expressed as its partial pressure, in kPa.) This is called an oxygen
dissociation curve. The curve is S-shaped. This tells us that the first oxygen molecule
attaches with difficulty. This is because the addition of the first oxygen molecule has to
slightly distort the shape of the haemoglobin molecule. However, once this has occurred,
the second oxygen molecule combines slightly more easily and then the third and forth
combine progressively more easily. This sequence of changes accounts for the S-shape of
the curve.
the dissociation curve of human haemoglobin
at body temperature
haemoglobin 100 20
four sub-units interlocked
oxygen concentration/cm3 per 100 cm3 of blood
saturation of haemoglobin with oxygen/%
to form a compact molecule 90 18
80 16
70 14
haem group 60 12
(non-protein)
50 10
40 8
O2 retained here
30 6
20 4
globin (protein)
Figure 8.10 The 10 2
structure of A combination of protein and non-protein 0 0
haemoglobin and its means that haemoglobin is a conjugated 0 2 4 6 8 10 12 14
protein. oxygen concentration, pO2/kPa
affinity for oxygen
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EXTENSION
8 Carbon monoxide poisoning
Carbon monoxide is found in vehicle exhaust gas, cigarette smoke, and as a product
of incomplete combustion of natural gas where there is restricted access for air.
Carbon monoxide combines irreversibly with the iron of haemoglobin at the site
that oxygen would otherwise occupy, forming carboxyhaemoglobin. The affinity of
carbon monoxide for haemoglobin is about 300 times greater than oxygen’s and at
low partial pressures of this poison the blood’s ability to t ransport oxygen may be
fatally reduced.
(Incidentally, a catalytic converter, when fitted to a vehicle’s exhaust, can
significantly reduce the quantity of the gas by oxidising it to carbon dioxide.)
100 Most haemoglobin molecules are fully saturated at

the oxygen dissociation curve
of haemoglobin at the CO2 a partial pressure of oxygen of only 8 kPa so oxygen
90
concentration of the blood in is efficiently loaded under the conditions in our
transit around the body,
ventilated lungs.
saturation of haemoglobin with oxygen/%
80
i.e. about 5.3 kPa CO2
70
the oxygen dissociation curve
Bohr effect
60 of haemoglobin at the CO2 In respiring tissue the situation is quite different.
concentration around respiring
55
cells, i.e. about 9.3 kPa CO2
Here the partial pressure of oxygen is much lower
50
because oxygen is used in aerobic respiration.
40
as the CO2 concentration Oxyhaemoglobin will dissociate if the partial
increases, more O2 is
35 released from haemoglobin
pressure is less than 8 kPa, making oxygen molecules
30 (Bohr effect) readily available for use in the cells of respiring
tissues.
20
15 So oxygen is scarce in respiring cells and the
10 concentration of carbon dioxide is high. In this
environment the concentration of carbon dioxide
0
0 2 2.7 4 6 8 10 12 14 has a marked effect on the loading and unloading of
oxygen concentration, pO2/kPa oxygen by haemoglobin.
pO 2 in
pO 2 in
respiring An increased carbon dioxide concentration shifts the
lungs
cells oxygen dissociation curve to the right. That is, where
the carbon dioxide concentration is high (in the
▲ Figure 8.11 Bohr effect
actively respiring cells), oxygen is released from oxyhaemoglobin even more readily.
– how carbon dioxide
favours the release This very useful outcome is known as the Bohr effect (Bohr shift).
of oxygen in respiring
tissues Carbon dioxide
Carbon dioxide is transported in the blood, in both the plasma and in red blood cells,
mainly as hydrogencarbonate ions.
Question
carbonic anhydrase
6 Use Figure 8.11 to CO2 1 H2O HCO3 1 H1
deduce the change
in the percentage The enzyme carbonic anhydrase, which catalyses this reaction, is present in the red
saturation of blood cells. You can see that hydrogen ions are one of the products. The hydrogen ions
haemoglobin if the released become associated with haemoglobin to form haemoglobinic acid. In effect,
partial pressure of the haemoglobin molecules act as a buffer for hydrogen ions, preventing the blood from
oxygen drops from becoming acidic (Figure 8.12).
4 to 2.7 kPa when
the partial pressure The chloride shift
of carbon dioxide is Charged ions such as H+ and HCO3− are usually unable to pass through the plasma
5.3 kPa. membrane, but red blood cells can exchange bicarbonate ions for chloride ions using an
anion exchanger protein embedded in their membranes.
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As the hydrogen carbonate ions (HCO3−) diffuse out of the red blood cells, there is an
increasing positive charge inside the cell. Negatively charged chloride ions (Cl−) move
into the red blood cell to balance out the charges, returning the pH to neutral; this is
called the chloride shift. The chloride shift prevents the blood from becoming too acidic.
8
In addition, about 5 per cent of the carbon dioxide remains as carbon dioxide in the blood,
dissolved in the plasma. A further 10 per cent combines with haemoglobin, reacting with
amine groups (–NH2) to form carbaminohaemoglobin. In the lungs, the partial pressure
of carbon dioxide (pCO2) there allows these forms of carbon dioxide to be released, also.
air in alveolus plasma
8.3 The heart

O2 in high concentration O2 in incoming air diffuses into red blood cells and combines
CO2 in low concentration with haemoglobin (HHb) to form oxyhaemoglobin (HbO2)
O2 + HHb HbO2 + H+
O2
in the lungs
CO2 HCO3– + H+
H2O + CO2
carbonic anhydrase hydrogencarbonate ions
combine with H+ in the
CO2 diffuses into red cell presence of carbonic
the air in the alveolus hydrogencarbonate ions diffuse anhydrase to form water and CO2
into red blood cells and are converted
to carbon dioxide gas
moved by the pumping action

of the heart
tissue fluid
O2 in low concentration
CO2 in high
concentration
in the respiring tissues

CO2 + H2O HCO3– + H+
carbonic anhydrase CO2
H+ + HbO2 HHb + O2
as oxyhaemoglobin gives up O2
O2 it becomes basic (accepts H+
ions) and thus acts as a pH buffer
▲ Figure 8.12 The transport of oxygen and carbon dioxide between the lungs and respiring tissues
8.3 The heart

Learning outcomes
8.3.1 describe the external and internal structure of the mammalian heart
8.3.2 explain the differences in the thickness of the walls of the: atria and
ventricles, and left ventricle and right ventricle
8.3.3 describe the cardiac cycle, with reference to the relationship between
blood pressure changes during systole and diastole and the opening and
closing of valves
8.3.4 explain the roles of the sinoatrial node, the atrioventricular node and the
Purkyne tissue in the cardiac cycle (knowledge of nervous and hormonal
control is not expected)
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Starting point
8 ★ The mammalian heart is a double pump: the right side pumps blood at low
pressure to the lungs and the left side pumps blood at high pressure to the
rest of the body.
The heart as a pump

The human heart is the size of a clenched fist. It lies in the thorax between the lungs and
below the breast bone (sternum). The heart is a hollow organ with a muscular wall. It is
contained in a tightly fitting membrane, the pericardium – a strong, non-elastic sac

which anchors the heart within the thorax and prevents the overfilling of the heart with
blood. Within the pericardium is fluid which reduces friction between the beating heart
muscle and the surrounding tissues.
The wall of the heart is supplied with
oxygenated blood from the aorta via
striations
coronary arteries. All muscle tissue consists of
cells called fibres that are able to shorten by a
half to a third of their length. Cardiac muscle
consists of cylindrical branching columns of
fibres, uniquely forming a three-dimensional
network and allowing contractions in
nucleus three dimensions. The fibres have a single
nucleus, are striped or striated and are
surrounded by sarcolemma (muscle cell
branch
surface membrane) (Figure 8.13). They are
very well supplied by mitochondria and
sarcolemma capillaries. The impulse to contract is
(plasma
membrane of
generated within the heart muscle itself
muscle fibre) (known as a myogenic origin), not by nervous
stimulation (a neurogenic origin). Heart
muscle fibres contract rhythmically from their
▲ Figure 8.13 Cardiac formation until they die.
muscle
Structure of the heart chamber walls in relation to function
The cavity of the heart is divided into four chambers (Figure 8.14). The chambers of the
right side of the heart are separated from those of the left side by a wall of muscle called
the septum.
The upper chambers are thin-walled and are called atria (singular: atrium). These
chambers receive blood into the heart under relatively low pressure. Later, when the
walls of the atria contract, the blood they now contain is pumped into the ventricles.
At this stage the ventricles are in a relaxed condition – there is little resistance to this
inward flow of blood.
The two lower chambers are thick-walled and called ventricles. They eventually pump
the blood out of the heart – the left ventricle pumps blood through the entire systemic
circulation, whereas the right ventricle pumps blood through the pulmonary circulation.
Consequently, the muscular wall of the left ventricle is much thicker than that of the right
ventricle, for it has to overcome the greater resistance of the capillaries throughout the
body tissues in comparison with a lower resistance in the lungs. However, the volumes
of the right and left sides (the quantities of blood they contain) are identical.
The functions of the heart valves

The direction of blood flow through the heart is maintained by valves, because it is
the valves that prevent back-flow of the blood when the muscles of the chamber walls
contract. Figure 8.15 (page 182) shows the action of all the valves of the heart.
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The atrioventricular valves are large valves that separate the upper and lower chambers.
The edges of these valves are supported by tendons anchored to the muscle walls of the
ventricles below and which prevent the valves from folding back due to pressure from
the ventricles. The valves separating the right and left sides of the heart are individually
8
named – on the right side, the tricuspid valve and on the left, the bicuspid or mitral valve.
Valves of a different type separate the ventricles from pulmonary artery (right side) and
aorta (left side). These are pocket-like structures called semilunar valves, rather similar
to the valves seen in veins.
8.3 The heart

heart viewed from the front of the body with pericardium removed
vena cava
from head
right pulmonary aorta

artery
left pulmonary
artery
right pulmonary
veins left pulmonary
veins
coronary artery
coronary vein
vena cava
from lower
part of body
heart in LS
vena cava
from head
aorta
left pulmonary
artery
right pulmonary
artery left pulmonary
veins
left atrium
right atrium
semilunar
valves
vena cava
from lower bicuspid
part of body valves
left ventricle
tricuspid valve
right
ventricle
▲ Figure 8.14 The structure
of the heart
What causes the valves of the heart to open and close?

The heart valves are opened and closed by differences in the blood pressure caused by
alternating contraction of heart muscle, first in the atrial walls (atrial systole), then in the
ventricles (ventricular systole).
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» Valves open when pressure on the input side (caused by muscle contraction) exceeds
that on the output side.
8 » Valves close when pressure on the output side (caused by muscle contraction) exceeds
that on the input side – typically caused by relaxation of the muscles on the input side.
Heart valves allow blood flow in Atrial systole
one direction only. They are • Atrial walls contract – the pressure is raised in the atria
opened and closed by • Vena cavae and pulmonary veins are closed
differences in blood pressure. • Atrioventricular valves pushed open – blood flows into the ventricles
• They are opened when the • Ventricular walls relaxed – the pressure is low in the ventricles
pressure on the input side • High pressure in the aorta and pulmonary arteries (due to the elastic
(caused by muscle contraction) and muscle fibres in their walls) – the semilunar valves are shut
exceeds that on the output side.

• They are closed when the Ventricular systole
pressure on the output side • Ventricular walls contract strongly – the pressure is raised in
exceeds that on the input side. the ventricles
Typically caused by the • Atrioventricular valves are closed and semilunar valves are opened –
relaxation of muscle on the blood is pushed out into the aorta and the arteries are stretched
input side. • Atrial walls relax – the pressure falls in the atria
• The vena cavae and pulmonary veins are open – blood flows into
the atria
▲ Figure 8.15 The action of

the heart valves
Diastole – atrial and ventricular
• The muscles of the atrial and ventricular walls are
relaxed – the pressure in both atria and ventricles is low
• The semilunar valves shut – there is a passive flow of
blood from the veins into the atria and ventricles
The cardiac cycle

The cardiac cycle is the sequence of events of a heart beat, by which blood is pumped
Question all over the body. The heart beats at a rate of about 75 times per minute, so each cardiac
7 The edges of the cycle is about 0.8 seconds long. This period of ‘heart beat’ is divided into two stages
atrioventricular valves which are called systole and diastole. In the systole stage heart muscle contracts
have non-elastic and during the diastole stage heart muscle relaxes. When the muscular walls of the
strands attached chambers of the heart contract, the volume of the chambers decreases. This increases
which are anchored the pressure on the blood contained there. This forces the blood to a region where
to the ventricle walls pressure is lower. Valves prevent blood flowing backwards to a region of low pressure,
(Figure 8.14). What so blood always flows on through the heart.
is the role of these
Look at the steps in Figures 8.15 and 8.16. You will see that Figure 8.16 illustrates the
strands?
cycle on the left side of the heart only, but both sides function together, in exactly the
same way, as Figure 8.15 makes clear.
We can start with contraction of the atrium (atrial systole, about 0.1 second). As the
walls of the atrium contract, blood pushes past the atrioventricular valve, into the
ventricles where the contents are under low pressure. At this time, any back-flow of
blood from the aorta back into the ventricle chamber is prevented by the semilunar
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valves. Notice that back-flow from the atria into the vena cavae and the pulmonary
veins is prevented because contraction of the atrial walls seals off these veins. Veins also
contain semilunar valves which prevent back-flow here, too. 8
Next the ventricle contracts (ventricular systole, about 0.3 seconds). The high
pressure this generates slams shut the atrioventricular valve and opens the semilunar
valves, forcing blood into the aorta. A ‘pulse’, detectable in arteries all over the body,
is generated (see below).
The atrium then relaxes for the remainder of the cycle (atrial diastole, about
0.7 seconds).
8.3 The heart

This is followed by relaxation of the ventricles (ventricular diastole, about 0.5 seconds)
until the next contraction of the ventricles.
Each contraction of cardiac muscle is followed by relaxation and elastic recoil. The
changing pressure of the blood in the atria, ventricles, pulmonary artery and aorta
(shown in the graph in Figure 8.16) automatically opens and closes the valves.
2 ventricle ventricle and

muscles contract and atrium
atrium muscles
muscles relax, causing blood
relax, while the
pressure to close the
pressure of blood 3 blood flows
1 atrium atrioventricular valve and
in the aorta causes into the atrium
muscles contract, open the semilunar valves,
the semilunar valves and opens the
pushing blood past forcing blood into the aorta
to shut atrioventricular
the atrioventricular
valves as it starts
valve into the ventricle
ventricular systole to flow into the
‘lub’ ventricle
atrial diastole
(heart sound when
the atrioventricular
valves close)
‘dup’
(heart sound when the
semilunar valves close)
atrial and
atrial systole ventricular diastole
1 2 3
stage
atria
ventricles
14
12
10
semilunar valve
pressure/kPa
8 semilunar closes
valve opens aorta
left ventricle
6 left atrium
bicuspid
4 valve bicuspid valve
closes opens
2
pressure changes 0
in aorta, left
ventricle and left –2
atrium 0 1 2 3 4 5 6 7 8
time/s
▲ Figure 8.16 The

cardiac cycle
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Question Heart rate and the pulse
8 8 Examine the data on

The contraction of the ventricle walls forces a surge of blood into the aorta and the
pulmonary arteries come under great pressure. This volume of blood is called the stroke
pressure change during volume. Each surge stretches the elastic fibres in the artery walls (Table 8.2, page 170).
the cardiac cycle in The artery walls are distended as the surge passes, before the subsequent elastic recoil
Figure 8.16. Determine occurs. This is known as the pulse. Each contraction of the ventricles generates a pulse,
or suggest why:
so when we measure our pulse rate we are measuring our heart rate. We can measure
a pressure in the heart rate in the carotid artery in the neck or at the wrist, where an artery passes over a
aorta is always bone. Incidentally, the amount of blood flowing from the heart is known as the cardiac
significantly higher
output. At rest, our cardiac output is typically about 5 litres of blood per minute.
than that in the atria
b pressure falls cardiac output 5 stroke volume 3 pulse rate
most abruptly in
Pulsation of the blood flow has entirely disappeared by the time it reaches the
the atrium once
capillaries. This is due to the extensive nature of the capillary networks and to the
ventricular systole is
resistance the blood experiences as it flows through the capillary networks.
underway
c the semilunar valve
in the aorta does not
Origin and control of the heart beat
open immediately The heart beats rhythmically throughout life, without rest, apart from the momentary
that ventricular relaxation that occurs between each beat. Even more remarkably, heart beats occur
systole commences naturally, without the cardiac muscle needing to be stimulated by an external nerve.
d when ventricular Since the origin of each beat is within the heart itself, we say that heart beat is
diastole commences, ‘myogenic’ in origin. However, the alternating contractions of the cardiac muscle of
there is a significant the atria and ventricles are controlled and co-ordinated precisely. Only in this way
delay before the can the heart act as an efficient pump. The positions of the structures within the
atrioventricular heart that bring this about are shown in Figure 8.17.
valve opens, despite The steps in the control of the cardiac cycle are as follows.
rising pressure in the
atrium » The heart beat originates in a tiny part of the muscle of the wall of the right
e it is significant that atrium, called the sinoatrial node (SA node) or pacemaker.
about 50 per cent of » From here a wave of excitation (electrical impulses) spreads out across both atria.
the cardiac cycle is » In response, the muscle of both atrial walls contracts simultaneously (atrial systole).
given over to diastole. » This stimulus does not spread to the ventricles immediately because of the
presence of a narrow band of non-conducting fibres at the base of the atria. These
block the excitation wave, preventing its conduction across to the ventricles.
stimulation of heart beat Instead, the stimulus is picked up by the atrioventricular node (AV node),
originates in the muscle situated at the base of the right atrium.
sinoatrial
» After a delay of 0.1–0.2 seconds, the excitation is passed from the
node atrioventricular node to the base of both ventricles by tiny bundles of
(pacemaker) conducting fibres known as the P urkyne tissue. These are collectively
in right
atrium
called the bundles of His.
» On receiving this stimulation from the bundles of His, the ventricle muscles
start to contract from the base of the heart upwards (ventricular systole).
spread of » The delay that occurs before the atrioventricular node acts as a ‘relay
electrical station’ for the impulse permits the emptying of the atria into the
activity
through ventricles to go to completion and prevents the atria and ventricles from
atrioventricular heart muscle contracting simultaneously.
node
» After every contraction, cardiac muscle has a period of insensitivity to
stimulation, the refractory period (a period of enforced non-contraction –
diastole). In this phase, the heart begins to refill with blood passively. This
refractory period allows the heart to refill with blood and stops it beating
too quickly, which could cause the cardiac muscle to fatigue, and also
Purkyne stops the heart muscle from remaining involuntarily contracted, which
fibres
would be fatal.
▲ Figure 8.17 Myogenic origin of the The heart’s own rhythm, set by the sinoatrial node, is about 50–60 beats per
heart beat minute. Conditions in the body can and do override this basic rate and increase
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heart performance. The action of the pacemaker is modified according to the needs of
the body. For example, it may be increased during physical activity. This occurs because
increased muscle contraction causes an increased volume of blood passing back to the
heart. The response may be more powerful contractions without an increase in the rate
8
of contractions. Alternatively, the rate of 75 beats per minute of the heart ‘at rest’ may be
increased to up to 200 beats a minute during very strenuous exercise.
EXTENSION
8.3 The heart

Electrocardiography
The impulses (action potentials) that originate in the sinoatrial node (pacemaker) of the heart during the cardiac
cycle produce electrical currents that are also conducted through the fluids of the body as a whole and can be
detected at the body surface by electrocardiography. Here, electrodes are attached to the patient’s chest and the
electrical activity detected is displayed as an electrocardiogram (ECG) by means of a chart recorder (Figure 8.18).
Electrocardiography has clinical applications; it is an aid in the diagnosis of cardiovascular disease (CVD).
Some heart conditions that can be detected by the analysis of electrocardiograms are listed in Table 8.7.
normal electrocardiogram (ECG), analysed
Key
R
1.0
atrial contraction (atrial systole)
ventricular contraction (systole)
P wave atrial depolarisation – leads to

S–T atrial contraction
0.5
segment
P–R interval time for impulse to be conducted
millivolts (mV)
from SA node to ventricles, via

T AV node
P
QRS complex onset of ventricular depolarisation –
0 leads to ventricular contraction
T wave ventricular repolarisation –

P–Q Q relaxation phase
interval
S
–0.5 Q–T interval
0 0.2 0.4 0.6 0.8

seconds
abnormal traces showing
1 tachycardia
heart rate is over
100 beats/minute
2 ventricular fibrillation
uncontrolled contraction
of the ventricles – little
blood is pumped
3 heart block
ventricles not always electrical activity detected through electrodes attached to
stimulated the patient’s chest is displayed on the computer as an
electrocardiogram
▲ Figure 8.18 Electrocardiography (Continued)
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8
Heart conditions detected by abnormal ECG traces
Tachycardia A normal adult heart beats between 60 and 100 times a minute; a heart rate over 100 beats a
minute is called tachycardia.
Tachycardia may be relatively harmless and need no treatment but some forms can be life-
threatening.
Ventricular Asynchronous contraction of the ventricle muscle fibres results in a failure of the heart to pump
fibrillation sufficient blood because some muscle fibres are contracting while others are relaxing.
Heart block The most common site of blockage is at the atrioventricular node.
Arrhythmia Arrhythmia is a condition of irregularity in heart rhythm due to a defect in the conduction system
of the heart. It may be due to:
• drugs, such as nicotine or alcohol
• anxiety, hypothyroidism or potassium deficiency.
▲ Table 8.7 Heart conditions detected by ECG analysis
SUMMARY
» Mammals have a closed circulation in which hydrogencarbonate ions. These are transported
blood is pumped by a muscular heart through a mainly in the plasma.
continuous series of tubes – the arteries, veins » The heart is a hollow, muscular organ of four
and capillaries. It is a double circulation in that chambers. The right and left halves of the heart
blood goes twice through the heart in every are completely separate. The upper chambers,
complete circulation. The pulmonary circulation the atria, have relatively thin walls. The lower
is to the lungs, supplied by the right side of the chambers, the ventricles, have thick walls. The
heart. The systemic circulation is to the rest of the thickness of the wall of the left ventricle is much
body, supplied by the left side of the heart. greater than the right because the left ventricle
» Blood consists of a straw-coloured fluid, the has to pump blood all around the rest of the
plasma, and blood cells. In humans, red blood body whereas the right ventricle pumps blood
cells (erythrocytes) are without a nucleus, contain only to the lungs which are very close to the
haemoglobin and transport oxygen. White blood heart. Direction of blood flow through the heart
cells (leucocytes) combat disease. They are is maintained by valves.
circulated by the blood to locations in the body » The cycle of changes during a heart beat, known
where they act. as the cardiac cycle, lasts about 0.8 seconds
» Tissue fluid is the liquid that bathes all the body when the body is at rest. It consists of alternate
cells, formed from the blood plasma that has contraction (systole) and relaxation (diastole).
escaped from the capillaries. This fluid differs from Atrial systole precedes ventricular systole and
plasma in that blood cells and plasma proteins are both are followed by periods of diastole that partly
absent. Lymph is the tissue fluid that drains back overlap. Then atrial systole commences again.
into the blood circulation via the lymphatic system » The heart beat originates in the heart itself
(lymph vessels and nodes). (myogenic), at the sinoatrial node (SAN or
» The main role of the blood circulation is the pacemaker) in the upper wall of the right atrium.
transport of respiratory gases, water, nutrients, This activates the atrial muscle to contract and
waste products, heat and hormones. The transfer triggers the atrioventricular node (AVN), which
of substances in solution or suspension is carries the signal to contract on to the ventricles.
essential since diffusion is insufficient. The excitation passes from the atrioventricular
» Haemoglobin, a conjugated protein, and the node to the base of both ventricles by tiny bundles
enzyme carbonic anhydrase occur in red of conducting fibres, known as the Purkyne
blood cells and together affect the transport of tissue. These are collectively called the bundles
respiratory gases. Oxygen is transported as of His. Impulses from the cerebral hemispheres
oxyhaemoglobin. Haemoglobin buffers the H1 or involuntary reflexes from stretch receptors in
ions from the reaction of carbon dioxide and arteries outside the heart, or hormone action can
water in which carbon dioxide is converted to all alter the rate at which the heart beats.
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1 Fig. 1.1 is a graph showing how the blood pressure in the pulmonary artery and in 8
the right ventricle changes during one cardiac cycle.
4 Key
blood pressure/kPa
pulmonary artery
3
right ventricle
2

1
0
0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8
time/s
▲ Fig. 1.1
a Use Fig. 1.1 to state the time at which:

i the valve between the right ventricle and the pulmonary artery closes. [1]
ii the ventricle begins to contract. [1]
b State and explain the similarities and differences between Fig. 1.1 and
a graph showing how the blood pressure for the left ventricle changes
during the same cardiac cycle. [4]
[Total: 6]
(Cambridge International AS and A Level Biology 9700 Paper 21 Q2b Oct/Nov 2017)
2 a What tissue is found in all types of blood vessel? How it is adapted to its
functions? [4]
b In a table, give the differences between the structure of an artery and a
vein as seen in transverse section. [4]
c Explain the difference between a single and a double circulation, and the
benefits gained by respiring tissues served by the latter. [2]
d In a table, compare the similarities and differences in composition between
plasma and tissue fluid. [4]
e List in order the pathway of vessels and chambers taken by a red blood
cell from the vena cava until it reaches cells of the muscles of the arm. [6]
[Total: 20]
3 Both red blood cells in mammals and companion cells in flowering plants play a
part in internal transport. Describe the mature structure of both these cells, and
how those structures are adapted to deliver their precise roles.
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AS LEVEL
9 Gas exchange
9 Gas exchange
The gas exchange system is Learning outcomes

responsible for the uptake
of oxygen into the blood
and the excretion of carbon 9.1.1 describe the structure of the human gas exchange system, limited to:
dioxide. An understanding of lungs, trachea, bronchi, bronchioles, alveoli and capillary network
this system shows how cells, 9.1.2 describe the distribution in the gas exchange system of cartilage, ciliated
tissues and organs function epithelium, goblet cells, squamous epithelium of alveoli, smooth muscle
together to exchange these and capillaries
gases between the blood
9.1.3 recognise cartilage, ciliated epithelium, goblet cells, squamous
and the environment.
epithelium of alveoli, smooth muscle and capillaries in microscope slides,
photomicrographs and electron micrographs
9.1.4 recognise trachea, bronchi, bronchioles and alveoli in microscope slides,
photomicrographs and electron micrographs and make plan diagrams of
transverse sections of the walls of the trachea and bronchus
9.1.5 describe the functions of ciliated epithelial cells, goblet cells and mucous
glands in maintaining the health of the gas exchange system
9.1.6 describe the functions in the gas exchange system of cartilage, smooth
muscle, elastic fibres and squamous epithelium
9.1.7 describe gas exchange between air in the alveoli and blood in the capillaries
Starting point
★ The gas exchange surface in the lungs is extensive, very thin, well supplied with
blood and well ventilated. The trachea and bronchi provide little resistance to
the movement of air to and from the alveoli.
mitochondrion –
9.1 The gas exchange system
organelle in which
some of the steps
Gaseous exchange – meeting the needs of respiration
CO2 O2 of energy transfer Living things need energy to build, maintain and repair body
cell surface occur (page 251)
membrane structures and also for activities such as metabolism, excretion,
and movement. Respiration is the process that transfers that
energy. Respiration occurs continuously in living cells, largely
in the mitochondria (Topic 1). Most respiration is aerobic and
outside cell inside cell requires oxygen to transfer energy from carbohydrates and lipids.
low CO2 concentration, high CO2 concentration, Respiration results in the formation of ATP which is the energy-
high O2 concentration low O2 concentration
transferring molecule used in metabolic processes in cells. Carbon
dioxide is released as a waste product. This gas exchange in cells
O2 CO2 occurs by diffusion. For example, in a cell respiring aerobically
there is a higher concentration of oxygen outside the cells than
inside and so there is a net inward diffusion of oxygen (Figure 9.1).
CO2 O2
Respiratory systems in large animals

In larger animals most if not all of their cells are too far from
O2 CO2
the surface of the body to receive enough oxygen by diffusion
▲ Figure 9.1 Gas exchange in an animal cell alone. Remember, the surface area to volume ratio decreases as
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Questions the size of an organism increases. In addition, many of these animals have developed
an external surface that provides protection for the body. This is true of water-tight
1 List three factors
affecting the rate
(impervious) outer coverings and tough or hardened skins. These outer surfaces are no
longer suitable for gas exchange and the organism requires an alternative respiratory
9
of diffusion across surface. Active organisms have an increased metabolic rate, too, and the demand for
a surface and oxygen in their cells is higher than in slow-moving or inactive organisms. So we find
explain why each that, for many reasons, larger active animals have specialised organs for gas exchange.
is significant. (You
may need to refer to Efficient respiratory surfaces in animals take various forms, such as the gills of fish, the
Table 4.1, page 87.) lungs of mammals, the tubular system of many insects that carries air to the most actively

2 Due to the presence respiring organs. All these systems provide a large thin surface area, suitable for gas
of haemoglobin, exchange. In addition, conditions for diffusion are often improved by three refinements.
about 20 cm3 of 1 A ventilation mechanism – a pumping mechanism that moves the respiratory
oxygen is carried medium (water or air) over the gills or into and out of the lungs or tubes. This
per 100 cm3 of maintains the concentration gradient for diffusion.
blood. By contrast, 2 A blood circulation system – a means of speeding up the transport of dissolved
the solubility of oxygen from the respiratory surface as soon as it has diffused in. This, too, maintains
oxygen in water is the concentration gradient.
only 0.025 cm3 per 3 A haem protein, such as haemoglobin, that can associate with oxygen and so
cm3 under the same increase the gas-carrying ability of the blood. For example, we have seen that our
conditions. How blood contains red blood cells packed with the respiratory pigment haemoglobin
much more oxygen (Figure 8.10, page 177).
is carried by a litre
(1000 cm3) of blood The structure of the human gas exchange system
compared with the
We can now consider the human lungs as structures adapted for rapid gas exchange.
same quantity of
The structure of the human thorax is shown in Figure 9.2.
water?
The lungs are housed in the thorax, an air-tight, dome-shaped chamber formed by
the rib cage and its muscles, and its domed floor, the diaphragm. The diaphragm is
a sheet of muscle attached to the body wall at the base of the rib cage, separating the
thorax from the abdomen. The internal surfaces of the thorax secrete and maintain
pleural fluid. Pleural fluid is a lubricating liquid made from the blood plasma. This fluid
provides the surface tension that holds the lungs to the rib cage and protects the lungs
from friction during breathing movements.
nasal cavity
palate
buccal cavity
pharynx
epiglottis
larynx
oesophagus
trachea
ribs (in section)
bronchus
pleural fluid
position of
the heart
lung
diaphragm
bronchioles
abdominal
cavity
▲ Figure 9.2 The structure of the human thorax
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The lungs connect with the pharynx at the rear of the mouth by the trachea. Air reaches
the trachea from the mouth and nostrils, passing through the larynx (‘voice box’). Entry
9 into the larynx is via a slit-like opening, the glottis. Above it is a cartilaginous flap, the
epiglottis. Glottis and epiglottis work to prevent the entry of food into the trachea.
The trachea then divides into bronchi, one to each lung. Within the lungs the bronchi
continue to divide into smaller bronchi, a branching system referred to as the ‘bronchial
tree’. The smallest bronchi themselves divide into bronchioles. The finest bronchioles, the
terminal bronchioles, end in air sacs – the alveoli. A capillary network wraps around the
clusters of alveoli.
9 Gas exchange
Trachea, bronchi and bronchioles – structure in relation to function

To protect the delicate lining of the alveoli, the air reaching them needs to be warmed
(preferably to body temperature), to be moist and to be as free of dust particles and
other foreign bodies as possible. In the nostrils, hairs trap and filter out large dust
particles from the incoming air stream. Superficial blood vessels in the nostrils start to
warm the incoming air. The trachea and bronchi are lined with a ciliated epithelium
with numerous goblet cells (Figure 9.3). The sticky mucus produced here moistens
the incoming air and traps finer dust particles. The ciliated epithelium beats the mucus
stream up into the buccal cavity, where it is swallowed.
SEM showing that the lining of the bronchioles is of simple, ciliated
columnar epithelium, with mucus secreted by goblet cells (×6000)
drawing of the ciliated epithelium cells with goblet cells (HP)
cilia
simple, columnar epithelium
cell
goblet cell
mucus
nucleus
cytoplasm
basement membrane
▲ Figure 9.3
Ciliated The trachea lies beside and in front of the oesophagus (the ‘food tube’). Any hard mass
epithelium of food passing down the oesophagus might interrupt the air supply to the lungs.
with goblet Incomplete rings of cartilage in the trachea wall prevent collapse under pressure from
cells a large bolus passing down the oesophagus (Figure 9.4).
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The walls of the bronchi and larger bronchioles, in addition to rings or tiny plates of
cartilage, also contain smooth muscle. At each division of the bronchial tree the amount
of cartilage decreases and the amount of smooth muscle increases. Together they
prevent collapse of these tubes – collapse might be triggered by the sudden reduction in
9
pressure that occurs with powerful inspirations of air, for example. The smooth muscles
also regulate the size of the smaller airways as the muscle fibres contract or relax.
The walls of the smaller bronchioles are without cartilage (Figure 9.5, overleaf). These
tubes, the narrowest of the airways serving the alveoli, branch repeatedly and, as they do
so, become progressively narrower. Here, smooth muscle is the major component of their

walls and the lining of columnar epithelium contains only very occasional goblet cells.
So the air sacs are supplied with warm moist clean air for gaseous exchange, but of
course the lungs cannot prevent some water loss during breathing – a significant issue
for most terrestrial organisms (Figure 9.6, overleaf).
photomicrograph of trachea in TS (ë10)
lining of ciliate
epithelium with
goblet cells
region of loose tissue

with mucus-secreting
glands and blood vessels
smooth muscle joining

cartilage ends
incomplete (C-shaped)
cartilage ring
photomicrograph of part of wall of trachea,

HP (ë50) with interpretive drawing
cilia + columnar epithelium

with goblet cells
region of mucus-secreting
glands and blood vessels
smooth muscle
part of C-shaped
cartilage ring
connective tissue
▲ Figure 9.4 The structure of the trachea
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9
lumen of bronchiole
9 Gas exchange
lining of columnar epithelium

(goblet cells are rare here)
smooth muscle makes up

the bulk of the wall
(cartilage is absent here)
surrounding the bronchiole
are numerous alveoli
▲ Figure 9.5 The structure of a small bronchiole
Questions Exhaled air is saturated with

water vapour, an invisible
component except in freezing
3 Draw and label a weather or when breathed on to
low-power plan of a very cold surface.
a representative
part of the wall The water balance of the
of the bronchiole, body:
• about 3 litres is taken in and
as see under lost daily
high power • about 10–15% of this total is
magnification in lost from the lungs.
Figure 9.5.
4 What percentage water gain water loss
of our total daily
water loss occurs fluids drunk urine
from the lungs?
Explain why this
happens.
metabolic water from taken in evaporated from evaporated from faeces

respiration of sugar and solid food the skin the lungs
other respiratory substrates, e.g.
C6H12O6 + 6O2 6CO2 + 6H2O
▲ Figure 9.6 Water loss during gas exchange in humans
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EXTENSION
9
Bronchiole structure and asthma
Asthma is a disease of the airways of the lungs. In
an asthma attack, the bronchioles are narrowed by
excessive contraction of the smooth muscle in their
walls. Immediately, getting air into and out of the lungs
becomes difficult. Also, extra mucus is produced,
exaggerating the symptoms. Breathing can become very

difficult indeed.
Asthma attacks may be started by the arrival of irritants
like pollen, dust from pets or droppings from house dust
mites. Certain viruses and the oxides of nitrogen present
in vehicle exhaust fumes may also be triggers.
▲ Figure 9.7 Asthma
patient using an During times of physical activity our involuntary
inhaler nervous system naturally releases hormones that relax
the smooth muscles of the bronchioles, dilating them
so that air reaches the alveoli more quickly. Medical treatments for asthma sufferers
seek to trigger this relaxation, too (Figure 9.7).
Alveolar structure and gaseous exchange

Question
The lung tissue consists of the alveoli, arranged in clusters, each served by a tiny terminal
5 Explain the bronchiole. Alveoli and the terminal bronchioles have elastic connective tissue as an
difference between integral part of their walls. These fibres are stretched during inspiration, when the alveoli
gas exchange and are caused to expand, but recoil during expiration, aiding the expulsion of air as the
cellular respiration.
alveoli return to their resting condition (Figure 9.8).
smooth muscle
capillaries
On inspiration On expiration
• the volume of the • the volume of the thorax
thorax increases decreases
• the walls of the alveolus • the alveolus and terminal
elastic fibres and terminal bronchiole bronchiole revert to resting size,
are stretched due to recoil of the elastic fibres
• air is drawn in • air is expelled
terminal
bronchiole bands of overlapping
elastic fibres
alveolus
wall
alveolus
▲ Figure 9.8 The role of

elastic fibres in the
alveoli and bronchioles
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A capillary system wraps around the clusters of alveoli. Each capillary is connected to
a branch of the pulmonary artery and is drained by a branch of the pulmonary vein
9 (Figure 9.10, opposite). The pulmonary circulation is supplied with deoxygenated blood
from the right side of the heart and oxygenated blood is returned to the left side of the
heart to be pumped to the rest of the body (page 181).
There are some 700 million alveoli present in our lungs, providing a surface area of
about 70 m2 in total. This is an area 30–40 times greater than that of the body’s external
skin. The wall of an alveolus is formed by squamous epithelium, one cell thick. An
epithelium is a sheet of cells bound strongly together, covering internal or external
9 Gas exchange
surfaces of multicellular organisms. Lying very close is a capillary, its wall also just a
single, flattened (endothelium) cell thick. The combined thickness of walls separating
air and blood is typically 2–4 μm thick. The capillaries are extremely narrow, just wide
enough for red blood cells to squeeze through, so red blood cells are close to or in
contact with the capillary walls.
EXTENSION
Protective cells in the alveoli
The extremely delicate structure of the alveoli is protected by two types of cell,
present in abundance in the surface film of moisture (Figure 9.9).
» Macrophages (dust cells) are the main detritus-collecting cells of the body. They
originate from bone marrow stem cells and are then dispersed about the body
in the blood circulation. These amoeboid cells migrate into the alveoli from the
capillaries. Here these phagocytic white blood cells ingest any debris, fine dust
particles, bacteria and fungal spores present. They also occur lining the surfaces
of the airways leading to the alveoli.
» Surfactant cells produce a detergent-like mixture of lipoproteins and
phospholipid-rich secretion that lines the inner surface of the alveoli. This lung
surfactant lowers surface tension, permitting the alveoli to flex easily as the
pressure of the thorax falls and rises. It reduces a tendency of alveoli to collapse
on expiration.
surfactant cell that keeps

the alveolus wall flexible
(by a phospholipid
secretion) as the lungs
alternately stretch and alveolus
deflate in breathing wall
capillary
wall
blood cells
dust cell (macrophages)

that mops up dust and
bacteria
▲ Figure 9.9 Alveolus showing protective cells
Blood arriving in the lungs is low in oxygen (it has a lower partial pressure of oxygen
than the alveolar air – see Table 9.1) but high in carbon dioxide (it has a higher partial
pressure of carbon dioxide than the alveolar air). As blood flows past the alveoli, gaseous
exchange occurs by diffusion. Oxygen dissolves in the surface film of water, diffuses
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across into the blood plasma and into the red blood cells where it combines with
haemoglobin to form oxyhaemoglobin. At the same time, carbon dioxide diffuses from
the blood into the alveolus. 9
movement gaseous exchange in the alveolus
cartilage of air
rings capillary with
red blood cells
alveolar
blood supply to alveoli branch of membrane
pulmonary

vein O2
diffusion
branch of CO2
alveoli pulmonary
artery
branch of surface film
bronchus of water
capillary
network cartilage alveolus
rings
bronchioles
elastic connective tissue

occurs around the alveoli
photomicrograph of TS alveoli, HP
position of
capillary wall
(endothelium)
capillary
red blood
cells
alveolus
position of alveolar wall

elastic fibres (squamous epithelium)
▲ Figure 9.10 Gas exchange in the alveoli
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Questions Air flow in the lungs of mammals is tidal in that air enters and leaves by the same route.
Consequently there is a residual volume of air that cannot be expelled. Incoming
9 6 Create a table listing
the main structural
air mixes with and dilutes the residual air. The effect of this is that air in the alveoli
contains significantly less oxygen than the atmosphere outside (Table 9.1). Nevertheless,
features of the air the lungs are efficient organs of gaseous exchange.
sacs (alveoli) and
identifying the effects Inspired air Alveolar air Expired air
and consequence of
Oxygen 20% 14% 16%
each feature for gas
exchange. Carbon dioxide 0.04% 5.5% 4.0%
9 Gas exchange
7 If the concentration Nitrogen 79% 81% 79%

of carbon dioxide Water vapour Variable Saturated Saturated
were to build up
in the blood of a We have already noted that, in a mixture of gases, each component gas exerts a partial
mammal, why would pressure in proportion to how much is present. The partial pressure of oxygen is written as
this be harmful? p O2 and of carbon dioxide as p CO2.
At sea level, the atmospheric pressure is 101.3 kPa so, for example, the partial pressure of
oxygen in the air at sea level is:
pO2  101.3  20  20.3 kPa
100
but in the alveolus the partial pressure of oxygen is only:
pO2  101.3  14  14.2 kPa
100
▲ Table 9.1 The composition of air in the lungs
Observing and drawing plan diagrams of the gas exchange system

You will be required to observe and draw plan diagrams of the structure of the walls
of the trachea, bronchi, bronchioles and alveoli in which the distribution and roles
of cartilage, ciliated epithelium, and blood vessels are identified by your annotations.
Sources should include prepared slides observed by medium and high power,
photomicrographs and electron micrographs.
▲ Figure 9.11 TEM of the air–blood barrier in an alveolus/capillary section

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EXTENSION
Blood pressure and its measurement
9
By blood pressure we mean the pressure of the blood flowing through the arteries. We have noted that, initially,
flow is a surge or pulse (page 183). So it is arterial blood pressure that is measured, in a part of our body relatively
close to the heart. Blood pressure is quoted as two values (typically, one over the other). The higher pressure is
produced by ventricular systole (systolic pressure) and is followed by a lower pressure at the end of ventricular
diastole (diastolic pressure). Normally, systolic and diastolic pressures are about 15.8 and 10.5 kPa respectively.
(The medical profession give these values as 120 and 70–80 mmHg. The unit ‘mmHg’ was recognised as a unit of

pressure before the SI system was introduced.)
To measure these two values an inflatable cuff called a sphygmomanometer is used with a stethoscope, as shown
in Figure 9.12. The three steps are as follows.
1 The cuff is inflated and blood flow is monitored in the artery in the arm (the brachial artery) at the elbow.
Inflation is continued until there is no sound (indicating there is no flow of blood).
2 Air is now allowed to escape from the cuff, slowly, until blood can just be heard spurting through the
constriction point in the artery. This pressure at the cuff is recorded, as it is equal to the maximum pressure
created by the heart (the systolic pressure).
3 Pressure in the cuff is allowed to drop until the blood can be heard flowing constantly. This is the lowest
pressure the blood falls to between beats (the diastolic pressure).
Systolic pressure/mmHg Diastolic pressure/mmHg Condition Response

120 80 Optimum
120–129 80–84 Normal Biennial checks
130–139 85–89 High-normal Annual checks
140–159 90–99 Stage 1 hypertension Check in two months
160–179 100–109 Moderate (stage 2) hypertension Treatment essential
180–209 110–119 Severe (stage 3) hypertension if these conditions
persist
2101 1201 Very severe (stage 4) hypertension
▲ Table 9.2 Screening of blood pressure in adults
stethoscope blood flow in pressure how arterial pressure varies

artery stopped gauge systolic blood pressure
120 200
by pressure 160
in the cuff 80 240

The pascal (Pa) and its 70 20
300
120 mmHg = 16 kPa
multiple the kilopascal
(kPa) are generally
used by scientists to
measure pressure, but
in medicine the older arm 80 mmHg = 11kPa
unit of pressure, cuff
‘millimetre of mercury’ diastolic
(mmHg) is still used blood
(1mmHg = 0.13 kPa). brachial pressure
artery
hand pump
sphygmomanometer time
▲ Figure 9.12 Measuring blood pressure
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SUMMARY
9 » Gaseous exchange, the exchange of gases between bronchi and bronchioles, a branching system
an organism and its environment, makes possible referred to as the bronchial tree. The walls of
aerobic respiration in the cells of the body. these tubes are variously supported by cartilage
Gaseous exchange between individual cells and and smooth muscle and their surface is lined
their immediate environment occurs by diffusion. by a ciliated epithelium with goblet cells that
» Mammals, with their compact bodies and secrete mucus.
protected external surface, require specialised » Air is warmed and made moist as it is drawn into
9 Gas exchange
respiratory organs, the lungs. These efficient the thorax. Dust and foreign bodies are trapped
organs are housed in the air-tight thorax which in the mucus that is continually swept up and out
moves rhythmically to ventilate the lungs. The of the bronchial tree by the beating movements of
blood circulation system serves the lungs and the cilia.
transports oxygen all over the body, facilitated by » The millions of individual alveoli are served by
the respiratory pigment haemoglobin, present terminal bronchioles and both are thin walled
in the red blood cells. Carbon dioxide is returned and surrounded by fine capillaries. Here, a
to the lungs. huge, thin surface area is provided for efficient
» The alveoli (the air sacs where gaseous exchange of gases between the air and the blood
exchange occurs) are reached via the trachea, circulation.

1 Fig. 1.1 shows the first three structures of the human gas exchange system
through which air from the external atmosphere passes during inhalation.
Copy and complete Fig. 1.1 to show the pathway that air takes during inhalation. [2]
nasal cavity
pharynx
larynx
▲ Fig. 1.1
[Total: 2]
(Cambridge International AS and A Level Biology 9700 Paper 22 Q6a Feb/Mar 2016)
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2 As blood passes through the capillary network in the lungs, gas exchange occurs.
9
Describe the process of gas exchange between the alveolus and the blood. [4]
[Total: 4]
(Cambridge International AS and A Level Biology 9700 Paper 22 Q4d May/June 2016)
3 Smooth muscle and cartilage are two of the tissues found in the walls of
structures of the gas exchange system of mammals.
Copy and complete Fig. 3.1 to show the distribution of these tissues in the gas
exchange system of mammals. Choose from the four structures listed below. [3]

alveolus trachea bronchus bronchiole
irregular
plates and
incomplete
rings
cartilage
present
incomplete
present rings only
smooth cartilage
muscle absent
absent
▲ Fig. 3.1
[Total: 3]
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AS LEVEL
The infectious diseases Learning outcomes

studied in this topic are
caused by pathogens that
are transmitted from one 10.1.1 state that infectious diseases are caused by pathogens and are
human host to another. transmissible
Some, like Plasmodium 10.1.2 state the name and type of pathogen that causes each of the following
that causes malaria, are diseases: cholera – caused by the bacterium Vibrio cholerae; malaria –
transmitted by vectors, caused by the protoctists Plasmodium falciparum, Plasmodium malariae,
but there are many other Plasmodium ovale and Plasmodium vivax; tuberculosis (TB) – caused by the
methods of transmission,
bacteria Mycobacterium tuberculosis and Mycobacterium bovis; HIV/AIDS –
such as through water
caused by the human immunodeficiency virus (HIV)
and food or during sexual
activity. An understanding of 10.1.3 explain how cholera, malaria, TB and HIV are transmitted
the biology of the pathogen 10.1.4 discuss the biological, social and economic factors that need to be
and its mode of transmission considered in the prevention and control of cholera, malaria, TB and HIV
is essential if the disease (details of the life cycle of the malarial parasite are not expected)[
is to be controlled and
ultimately prevented.
Starting point
★ While many infectious diseases have been successfully controlled in some
parts of the world, many people worldwide are still at risk of these diseases.
10.1 Infectious diseases

What are ‘health’ and ‘disease’?
By disease we mean ‘an unhealthy condition of the body’. There are many different
diseases but good health is more than the absence of the harmful effects of disease-
causing organisms. We have already seen that illness may be caused by poor lifestyle
choices or unfavourable environmental conditions, such as lung cancer due to the
smoking of cigarettes. Diseases of this type are called non-communicable or non-
infectious diseases. Non-infectious disease may also be caused by malnutrition.
Inherited or genetic disorders such as sickle cell anaemia are included here, too.
Infectious diseases
In this topic the focus is on diseases that can be ‘caught’ – sometimes described as
contagious or communicable. These are infectious diseases. They are caused by
invading organisms living parasitically on or in the body. These disease-causing
organisms are known as pathogens. Pathogens may be viruses, some types of bacteria
or certain other organisms that are passed from one organism to another. The range of
pathogens is introduced in Figure 10.1.
The pathogens that cause some infectious diseases exist permanently in a particular
region or population. Such a disease is said to be endemic for it has a constant presence.
Malaria is an example – a serious threat to humans living in parts of Africa and other
tropical and sub-tropical regions in the world.
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bacterial disease cardiovascular diseases
e.g. tuberculosis
viral disease infectious diseases non-infectious

malnutrition
10
genetic diseases
e.g. influenza due to a disease- diseases not caught e.g. haemophilia,
causing agent from other organisms, sickle-cell anaemia
(typically a but rather due to
fungal disease microorganism) unhealthy lifestyles or
e.g. athlete’s foot passed between unfavourable respiratory diseases
organisms, environmental
directly or indirectly conditions cancer
protoctistan disease

e.g. breast cancer, lung cancer,
e.g. malaria
due to uncontrolled division of
cells, causing tumours
prions as disease agents
e.g. Creutzfeldt–Jacob disease (CJD) allergies and auto-immune diseases – overreaction
of our immune system can cause unpleasant or
dangerouse illness, e.g. asthma
▲ Figure 10.1 Types of human disease
On the other hand, epidemics are diseases that appear suddenly and then spread
rapidly in a specific area or within a particular population group for a time. Cases of
food poisoning are examples.
A pandemic disease is an epidemic that spreads far more widely – typically throughout
a whole country, a whole continent or throughout the whole world. It affects a huge
number of people. In the twentieth century several pandemics of influenza (’flu)
occurred. For example, the ’flu pandemic that occurred in 1918 was responsible for
10 million deaths worldwide.
In the prevention of infectious disease, knowledge of the biology of the pathogen is
essential. So the fight against disease involves the work of microbiologists as well as
the vigilance of the health professionals. In this topic, six specific infectious diseases of
humans are examined, most of which continue to present major threats to life. There
are reasons why this is so in the case of particular diseases but four general points are
significant.
» We live in a ‘global village’ world with speedy, worldwide travel facilities available
to some. A person, infected on one continent, may travel to another within hours –
before any symptoms have appeared.
» The human population is in a phase in which it is increasing more and more rapidly
(Figure 10.2, overleaf). In ever-increasing numbers, people congregate together –
many in mega-cities. Pathogens do not have far to travel.
» The work of health professionals is most effective where there is social stability, the
absence of war and an equitable division of wealth. Unfortunately, these conditions
are absent from many human societies.
» As natural resistance to pathogens develops and drugs to overcome them are found,
so pathogens themselves evolve greater infectivity – there is a continuing ‘arms race’
between pathogens and hosts.
Case studies in infectious disease

Cholera
Cholera is a dangerous disease, caused by the curved rod-shaped bacterium, Vibrio cholerae
(Figure 10.3, overleaf). This pathogen is typically acquired from drinking water that
has become heavily contaminated by the faeces of patients (or from human ‘carriers’ of
the pathogen). Alternatively, it may be picked up from food contaminated by flies that
previously fed on human faeces. The consumption of raw shellfish taken from waters
polluted with untreated sewage is another common source.
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time/years human population/millions
EXTENSION
10 Accidents
projected
at AD 2025
8500
present day 6250

Not included in 5200
any of the types of beginnings of the 610
ill-health listed in Industrial Revolution
Figure 10.1 is damage
due to accidents, such
as broken bones. A
bone fracture is not 1000 years ago 265

a disease but it is
certainly an unhealthy
condition of the body
which takes time to
repair. Clearly, there is
a borderline between
health and disease that 100
10 000 years ago
is not easy to define. (Neolithic Revolution) 4
Homo sapiens origins

(over 100 000 years ago)
▲ Figure 10.2 The changing pattern of the estimated world human population
Cholera is endemic in many parts of Africa, India, Pakistan, Bangladesh, and Central
and South America. A large number of the cholera bacteria must normally be ingested
for the disease to develop; fewer than 108 –109 organisms is ineffective (unless anti-
indigestion tablets that neutralise stomach acid were taken beforehand). Once the
bacteria has survived the stomach acid and reached the intestine, the incubation period
is from 2 hours to 5 days. However, 75 per cent of those infected develop no symptoms
at all – the bacteria merely remaining in their faeces for up to 2 weeks – while others
are made very ill. This difference may arise because there are different strains of the
▲ Figure 10.3 Scanning pathogen, some mild, others virulent in their impact on the patient.
electron micrograph of
Vibrio cholerae (×60 000) In the intestine, the pathogen increases in numbers and attaches itself to the epithelium
membrane. The release of a toxin follows. This generates symptoms in susceptible
patients that are mild to moderate in many people but extremely severe in about 20 per
cent of people who become infected.
The effect of this toxin is to trigger a loss of ions from the cells of the epithelium. Outflow
Question
of water follows and this is constantly replaced from tissue fluid. The patient rapidly loses
1 Digestion of the a massive amount of body fluid. Typically 15–20 litres may drain from the body as watery
proteins in the diarrhoea containing mucus and epithelium cells (‘rice-water stool’), as well as vast numbers
gut begins in the of the bacterium. At the same time, the patient has severe abdominal muscle cramp,
stomach. What is the vomiting and fever. Death may easily result from this dehydration because the severely
source and role of the reduced level of body fluids causes the blood circulation to collapse.
‘strong acid’ present
in the stomach when
food is ingested?
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gut epithelium Vibrio cholerae grow
connective tissue and reproduce in
10
lumen of gut
blood supply enterotoxin released

by V. cholerae
enterotoxin molecule
– a two-protein complex

enterotoxin binds
at receptor on
vomit receptor plasma membrane
enterotoxin affects The ‘bound’ enterotoxin:

vomit receptor (1) blocks pumps for Na+ ions uptake Na+ ions
into epithelium cells,
Na+ ions
Cl– ions
enterotoxin into – Cl– ions
(2) triggers hypersecretion of Cl ions from cells,
blood stream
H2O H2O
then, accumulation of Na+ and Cl– ions in H 2O
lumen causes water flow from
H2O
cells by osmosis
vomiting attacks temperature

triggered regulation centre
fluid and electrolyte loss
leading to fever
= diarrhoea
▲ Figure 10.4 The action of the cholera toxin
How the cholera toxin works

The cholera toxin consists of a two-protein complex composed of one ‘A’ subunit
and five ‘B’ subunits. The B part is the binding protein which attaches the toxin
complex to a particular site, a glycolipid, on the cell surface membranes of intestine
epithelium cells. The A part is an enzyme that activates other enzymes of the cell
surface membrane of the epithelium cell to which it is attached. These cause the
secretion of chloride ions into the gut lumen and inhibit any uptake of sodium ions.
Hypersecretion of chloride ions results and is followed by water loss (Figure 10.4).
Question Treatment of cholera

About 50 per cent of untreated cases of cholera are fatal but, when properly treated,
2 In cholera, toxic
generally less than 1 per cent of people are likely to die from this very unpleasant
protein triggers the
disease. A cholera patient requires immediate oral (by mouth) administration of a dilute
exit of chloride ions
solution of ions and glucose, present in a rehydration pack (Figure 10.5, overleaf), in
from the epithelium
cells into the lumen order to replace the fluids and ions lost from the body. The presence of glucose aids
of the gut. How does uptake of ions and compensates for energy loss. This solution prevents dehydration and
this movement of restores the osmotic balance of the blood and tissue fluid. This might seem a simple
ions differ from the process to people in the developed world but, in those places where cholera is endemic,
movement of water conditions may be very different. Many who contract the disease are weakened by
that follows ion shortage of food. Their drinking water may be of dubious purity and have to be carried
transport? some distance. The boiling of water makes it safe to use in the rehydration fluid but this
requires fuel that may be scarce.
Very severely dehydrated patients require the administration of intravenous fluids.
An additional treatment, the taking of the antibiotics streptomycin or tetracycline,
will assist in ridding the gut of the cholera cells. However, these drugs are of little use
unless fluid, ions and glucose replacement has succeeded in restoring normal body fluid
composition. An oral vaccine against cholera now exists but it is not effective against all
strains.
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Prevention of cholera
10 Cholera has been eradicated where there is effective sanitation. In the longer term,
the disease can be virtually eliminated by satisfactory processing of sewage and the
purification of drinking water, including a chlorination phase. In endemic areas, the
spreading of infection between households may be prevented by the boiling of drinking
water. The faecal contamination of foods by flies must also be prevented.
However, where populations have been displaced into inadequate overcrowded refugee
camps or have migrated to crowded urban slums where clean water and sanitation are
not available, cholera remains a threat to life (Figure 10.6). Malnourished children and
those living with HIV are at greatest risk.
▲ Figure 10.5 An oral

rehydration pack for the
treatment of cholera
▲ Figure 10.6 A refugee camp – ideal conditions for cholera
Pathogen Pathogen taxonomy A rod-shaped bacterium, Vibrio cholerae

Transmission Via polluted water and contaminated foods
Disease Incubation and Once in contact with the wall of the small intestine,
parameters venue a short incubation period of between 2 hours and
5 days
Signs, symptoms Diarrhoea, vomiting, abdominal muscle cramp, fever
and diagnosis Confirmation by microscopic examination of faeces
Treatment Replacement of lost water and ions by oral
rehydration with dilute solution of salts and
glucose
Prognosis Typically 50% of untreated cases are fatal but
with prompt correct treatment almost all patients
recover
Prevention and Boiling of drinking water, correct treatment of
control sewage and the prevention of food contamination
by flies
.
▲ Table 10.1 Cholera – the profile
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10
Key
malaria is

endemic in
tropical and
sub-tropical
regions
▲ Figure 10.7 World distribution of malaria
Malaria
Malaria is the most important of all insect-borne diseases, posing a threat to 2400 million
humans in 90 countries – 40 per cent of the world’s population, in fact (Figure 10.7).
About 80 per cent of the world’s malaria cases are found in Africa south of the Sahara.
Here, some 90 per cent of the fatalities due to the disease occur. It is estimated that
around 400 million people are infected, of which 1.5 million (mostly children under
5 years) die each year. Malaria kills more people than any other communicable disease,
with the exception of tuberculosis.
Malaria is caused by Plasmodium, a protoctist, which is transmitted from an infected
person to another by blood-sucking mosquitoes of the genus Anopheles. The mosquito is
described as the vector – an organism that transfers a disease or parasite from one host
organism to another. Of the four species of Plasmodium that cause malaria in humans, –
P. falciparum, P. malariae, P. ovale and P. vivax – only P. falciparum causes severe illness.
The others species trigger milder infections that are rarely fatal. Insecticides, particularly
DDT, had been effective against mosquitoes in the past but there has been a resurgence
of malaria since the 1970s.
Until 100 years ago, malaria was endemic in Europe and the USA, too. In Britain it was
called ‘fen ague’ because it was common in communities living near marshes and because
of the periodic shivering fits patients experienced. Marsh and fen drainage for agriculture
changed the environment so that it was no longer favourable to mosquitoes and their
transmission of the parasite. This is one reason for its disappearance in some areas.
Question
Transmission of Plasmodium by the mosquito
3 The insecticide Some pathogens need a vector to reach a new host. Stages in the life cycle of the pathogen
DDT is harmless may occur in the vector as well as the host. The female mosquito is the vector for malaria.
to humans at
(The male mosquito feeds on plant juices.) The mosquito is a fluid-feeding heterotroph, not
concentrations
a parasite, as sometimes stated. The female detects its human host, lands and inserts a long
that are toxic to
thin tube (called a proboscis) into a blood vessel below the skin surface. A ‘meal’ of blood
mosquitoes. This
insecticide is a is taken quickly; there is a danger that an active, alert human will ‘swat’ the intruder. For a
stable molecule blood-sucking insect, the mammalian’s blood-clotting mechanism presents a problem that
that remains active has to be overcome. This occurs when the mosquito’s proboscis penetrates the vein and a
long after it has secretion from its salivary glands passes into the victim’s blood, inhibiting it from clotting.
been applied and At this point Plasmodium may enter its human host (if the mosquito carries an infective
it is stored in the stage). Meanwhile, the mosquito loads up with a blood meal (Figure 10.8, overleaf).
body rather than Mosquitoes tend to feed at night, on sleeping victims. Those that alight on patients already ill
being excreted. with malaria are likely to be able to feed unhindered. The life cycle of the malarial parasite
Nevertheless, the use is complex. It consists of a sexual stage beginning in the human host (the primary host) and
of this compound has completed in the mosquito (the secondary host or vector). There is an asexual multiplication
been discontinued.
phase in the mosquito, too, and a phase of growth and multiplication in the liver cells and
Suggest why this is so.
red blood cells of the human host. Details of this life cycle are not required here.
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many immature
Plasmodium cells
malarial infection of a new patient
10
formed, and move
infected mosquito takes blood meal, to salivary glands
and delivers Plasmodium in the process within 6–12 days
blood drawn up as
'saliva' is discharged
down tube – stopping
clotting of victim's
blood
if a mosquito takes a
meal of blood now,
then fertilisation occurs
Plasmodium
(immature between Plasmodium transmission of malaria
liver gametes, once they are when mosquito then
stage) enters
liver cells within the insect host feeds on new victim
immediately
mature Plasmodium
cells pass into blood
and enter red cells; sexual cycle follows in red blood
asexual reproduction cells – male and female gametes
occurs here and parasites are released into blood
are released into the blood
in waves – every 48–72 hours
symptoms of malaria cycles of malaria symptoms (very high temperatures, headache,

are triggered each time nausea, enlarged, tender spleen) followed by relative normality
▲ Figure 10.8 Mosquito feeding and the transmission of malaria
Control measures
Control measures currently applied include the following.
» Interruption of the mosquito life cycle by attacking the larval stage which is an
air-breathing aquatic animal. Swamps are drained and open water sprayed with oil
(which forms a surface film, blocking the larva’s air tube), and with insecticide.
» Use of insecticides to kill adult mosquitoes on and around the buildings that humans
occupy.
» Protection from mosquito bites by sleeping under insecticide-treated mosquito nets
and by the burning of mosquito coils.
» Use of drugs to kill the stages of Plasmodium found in the blood and liver of infected
people.
» Use of drugs to kill Plasmodium as soon as it is introduced into a healthy person’s
blood by an infected female mosquito while feeding.
The effect of the sickle cell trait on death from malaria

The malarial parasite Plasmodium completes its life cycle in red blood cells but it cannot
do so in red blood cells containing haemoglobin-S (HbS) (Figure 16.27, page 370).
People with sickle cell trait are heterozygous for the sickle cell allele (HbA HbS). Their
red blood cells contain some sickle haemoglobin so they are protected to a significant
extent from malaria – they are much less likely to die from the disease. Where malaria
is endemic in Africa, possession of one mutant allele is advantageous. Consequently,
people with sickle cell trait are more likely to survive to pass on this allele to the next
generation (Figure 10.9).
How will malaria be eradiated?

After many soldiers in the wars of the first half of the twentieth century became
casualties of malaria, money was found for research into its control. Powerful
insecticides (first DDT, then gamma BHC and dieldrin) became available. By the 1960s
mosquito-eradication programmes had been successful in many countries. However, by
the 1970s, resistant strains of mosquito had appeared (and Plasmodium resistant to anti-
malaria drugs, too).
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distribution of haemoglobin-S is virtually the same as that of malaria
10
distribution of malaria caused by Plasmodium falciparum distribution of sickle cell gene in the population
or P. vivax (the forms of malaria that are most frequently
fatal, especially in childhood)

0–5%
5–10%
10–15%
15–20%
▲ Figure 10.9 The distribution of sickle cell trait in Africa confers an advantage
A determined search for a vaccine, begun in the 1980s, led to unsuccessful trials. Now
the situation is more hopeful. A huge injection of funds from the Gates Foundation into
this project occurred in 1994 and recently more has been pledged. The subsequent,
energetically pursued search for a vaccine that will confer lifetime active immunity for
treated humans has yielded several promising ‘candidates’. One is undergoing advanced
trials. The malaria research community remains cautious; the complex parasitic lifestyle
of Plasmodium makes it a difficult to eradicate and there have been many earlier set-backs.
In the longer term, control of mosquitoes by the careful use of selective insecticides will
be necessary, as well as the development of powerful vaccines, before this very well-
adapted malarial parasite is overcome.
Pathogen Pathogen taxonomy Plasmodium, a protoctist, with four species, of which P. falciparum is the most
dangerous
Transmission Via the blood meals of the female Anopheles mosquito
Disease Incubation and Plasmodium enters liver cells, reproduces asexually, then parasites are released into
parameters venue the patient’s blood stream and enter red blood cells immediately. A cycle of red blood
cell invasion, reproduction and release (with toxins) is then repeated.
Signs, symptoms A cycle of very high temperatures, headache, nausea and enlarged tender spleen every
and diagnosis 48–72 hours, followed by normality
Treatment A combination of anti-malarial drugs
Prognosis Most patients improve within 48 hours after initiation of treatment and become fever-
free after 96 hours
Infection by P. falciparum causes a form of malaria with a high mortality rate if
untreated
Prevention and Use of insecticides around human habitations
control Protection from insect bites, particularly by sleeping under insecticide-treated
mosquito netting
Destruction of the mosquito larva’s habitat by draining swamps and spraying open
water with oil to prevent larva’s access to oxygen via surface air tube
WHO Distribution Endemic in tropical and subtropical regions
status Global incidence About 219 million cases in 2017 with about 90% of the cases occurring in sub-Saharan
and mortality Africa
About 435 000 deaths in 2017 with the majority being young children in remote, rural
areas of Africa
▲ Table 10.2 Malaria – the profile
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Tuberculosis (TB)
10 Tuberculosis (TB), a major, worldwide public health problem of long standing, is
caused by a bacillus (rod-shaped bacterium) called Mycobacterium tuberculosis (Figure
10.10). Viewed under the microscope after staining by the Ziehl–Nielsen technique,
these cells appear bright red. This red colouration is unique to bacteria of the genus
Mycobacterium and is due to wax and other lipids in their walls. This is how the
▲ Figure 10.10 Electron pathogen is identified in infected patients.
micrograph of a colony
of Mycobacterium How tuberculosis spreads
tuberculosis (×25 000) People with pulmonary TB have a persistent cough. The droplets they inevitably
spread in the air are infected with live Mycobacterium (Figure 10.11). Tuberculosis
is chiefly spread by droplet infection in this way. Because of their lipid-rich cell
walls, the bacilli are protected from drying out so the pathogen may survive for
many months in the air and the dust of homes. This is another source of infection.
Overcrowded and ill-ventilated living conditions are especially favourable for the
transmission of the infection. However, it still requires quite prolonged contact
with a viable source before people will succumb, because the bacterium is not
strongly infectious.
A bovine form of TB caused by Mycobacterium bovis occurs in cattle and the bacillus
can enter the milk. Unpasteurised milk from infected cows is another potential source
of infection in humans. In some rural communities especially, this type of milk may
be consumed by both adults and children. Today, in some countries, milk is supplied
from ‘tuberculin-tested’ cows that are certified free of Mycobacterium. However, TB
may still be found in dairy herds. This is because of a ‘reservoir’ of the bacterium that
▲ Figure 10.11 Droplet exists in wild animals that have chance contacts with the herds. Treatment of milk by
infection pasteurisation is a major control mechanism as this heat treatment kills the bacteria
without affecting the quality of the milk.
How TB develops
Once inside the lungs, the bacteria are engulfed by macrophages in the alveoli and
bronchioles. If the person is in good health these white blood cells (with the help of
the T-lymphocytes which migrate in from lymph nodes – page 175) kill the pathogen.
Alternatively, and particularly with strains of Mycobacterium that are more infectious, the
pathogens may remain alive within the macrophage, although localised and effectively
controlled by the immune system. This explains why it is that not all infections with
M. tuberculosis result in TB – many people show no symptoms.
In fact, about one-third of the world’s population is infected
with M. tuberculosis, but only 5–10 per cent becomes sick or
infectious at some stage during their life.
However, if the patient is malnourished or is in inferior health
with a weakened immune system, a chronic infection may
develop, typically within the lungs. Cavities appear as bacteria
destroy the lung tissues. Blood vessels are broken down and
fluid collects. The structural damage to the lungs can be seen
X-ray examination (Figure 10.12).
The heart is visible as a white bulge, with

lung tissue on each side, enclosed in the rib
cage; the white patches clearly visible in the
yellow square contain live Mycobacterium
tuberculosis where lung structure and function
are permanently destroyed
▲ Figure 10.12 Chest X-ray showing TB in the lungs
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If the condition is not treated promptly, the pathogen may be carried in the bloodstream
and lead to TB in almost any part of the body. For example, the meninges of the brain,
bone tissue, the lymph glands, the liver, the central nervous system, the kidneys or the
genital organs can all be attacked. Generally, patients show loss of appetite, loss of weight,
10
excessive sweating and a decline in physical activity.
Treatment of TB
Today, TB is treatable but it is still a ‘killer’ disease if not diagnosed early on in the
infection. Among those with the disease of HIV/AIDS, TB is the leading cause of death.

Since TB is infectious, on confirmation of the diagnosis of a case of active tuberculosis,
all contacts of the patient need to be traced and screened by a community public health
team. Infectious patients require isolation and treatment with specific antibiotics until
they cease to cough up viable bacilli. Then, antibiotics continue to be administered to
the patient, now back in the community, until there is evidence the infection has been
eradicated from the body.
Unfortunately, microorganisms develop resistance to antibiotics and other drugs used
against them, with time. In the case of TB, this has already happened. Patients are now
treated with several antibiotics simultaneously because of the emergence of multidrug-
resistant TB (MDR-TB). This is particularly in the case of AIDs patients. MDR-TB is
especially common in the USA and South-East Asia (see Table 10.3, overleaf).
Prevention of TB
A vaccine against tuberculosis, the Bacillus Calmette–Guérin (BCG) vaccine, is prepared
from a strain of attenuated (weakened) live bovine tuberculosis bacillus, Mycobacterium
bovis. It is most often used to prevent the spread of TB among children.
A tiny quantity of inoculum is injected under the skin of the upper arm. Before
vaccination takes place, people are tested for existing immunity, since these people
will react unfavourably to the vaccine (the Heaf test, Figure 10.13). Only those with no
reaction may receive the vaccine. Immunity typically lasts for at least 15 years – longer
if the individual is re-exposed to TB bacilli, for example, by accidental encounter with
it. At best, the BCG vaccine is effective in preventing tuberculosis in a majority of people
for a period of 15 years. However, immunity wanes with time and disappears entirely
from the elderly.
1 instrument with six 2 after 2 or 3 days, if this test has proved 3 in a TB vaccination, the needle introduces
needles by which the skin is positive, i.e. the patient has TB or has already the BCG vaccine just below the skin – a blister
punctured and a small amount acquired immunity forms and eventually subsides, leaving the
of protein, extracted from TB patient protected against TB
bacilli, is introduced below the
skin (Heaf test)
▲ Figure 10.13 Heaf test and a TB vaccination
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How effective the vaccine is varies according to geography. Trials of BCG in two States
in the USA were only 14 per cent effective. Another trial showed no protective effect. In
10 the UK the vaccine is 80 per cent effective. How BCG vaccination is applied in different
countries is reviewed in Table 10.3.
Country Vaccination policy/recommended for

UK Babies born in areas of the UK where the rates of TB are high, or who have a parent or grandparent
who was born in a country where there’s a high rate of TB
Children under 16 who have recently arrived from countries with high levels of TB, or who have come
into close contact with somebody infected with respiratory TB

Those under the age of 35 whose occupation puts them at risk of exposure to TB
USA Not used
India and Introduced in 1948 – the first countries outside Europe to do so
Pakistan
Brazil Introduced in 1967
Malaysia Given once only, at birth, from 2001
Singapore Given once only, at birth, from 2001
Taiwan Given at birth and repeated at the age of 12
South Korea Recently discontinued altogether
USSR In the former USSR (including Russia) it was given regularly, throughout life
▲ Table 10.3 BCG vaccination policy recommended in various countries
Deaths from TB in England and Wales, 1900–2000 The changing pattern of the disease
upturn possibly attributable
decline attributable to There is evidence that TB was present in
to globalisation of
improvements in
housing provision
population movements, some of the earliest human communities
and appearance of and it has persisted as a major threat to
and diet for the poorest
70 bacilli resistant to available
people in health where vulnerable people lived in
drugs
society
crowded conditions. In the nineteenth
60
century, when the TB bacillus was first
identified, one in seven of all deaths
Annual death rate (thousands)
50
among Europeans was due to TB.
first anti-TB drug Today, in most developed countries this
40 treatments discovered
disease is relatively rare – in the UK for
30
BCG immunisation example, in 2007 the national average
programmes widely was about 15 cases per 100 000 of the
adopted
population. In these countries, the
20
reduction in TB throughout most of the
past century has been due to steadily
10
improving living conditions, particularly
in housing and diet (Figure 10.14).
0 However, today there is evidence of
1900 1920 1940 1960 1980 2000
a resurgence of the disease due to
Year
inward migration of new citizens, to
▲ Figure 10.14 How social, economic and medical factors have influenced the globalisation of travel and to the
the occurrence of TB in developed countries emergence of multidrug-resistant TB
(MDR-TB).
Globally, almost 14 million people have active TB, with approaching 2 million deaths
due to the bacillus annually. In developing countries with a high incidence of this
disease it primarily affects young adults. In developed countries where TB had ceased
to be a major health threat, the rising incidence of the disease is largely among those
described as immunocompromised (page 213), particularly those with HIV/AIDS, and
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among new migrants from developing countries – specially where they are now living in
poorer housing in large cities, such as New York and London.
10
The World Health Organization’s End TB strategy
The World Health Organization’s (WHO) End TB strategy aims to reduce TB deaths by
95 per cent, cut new cases by 90 per cent between 2015 and 2035, and to ensure that no
family is burdened with catastrophic expenses due to TB. It focuses on:
» integrated, patient-centred care and prevention – early detection, treatment and
prevention; ensuring that all patients have equal access to affordable services

» bold policies and supportive systems – strengthens health and social sector policies
and systems to prevent TB; supports universal health coverage and social protection;
and protects vulnerable groups such as the very poor, people living with HIV,
Question migrants, refugees and prisoners
4 Examine the data » intensified research and innovation – calls for an urgent boost in research
in Table 10.4 investments so that new tools can be developed and adopted in the next decade.
concerning the
disease TB in Selected WHO region Prevalence/rate per Mortality/rate per
selected WHO 100 000 of the population 100 000 of the population
regions. Then
suggest what factors Africa 231 37
are mostly likely to South-East Asia 220 32
account for these Europe 28 2.5
contrasting figures.
▲ Table 10.4 Estimated prevalence and mortality from TB in 2018 (WHO data)
Pathogen Pathogen A rod-shaped bacterium, Mycobacterium tuberculosis

taxonomy
Transmission Droplet transmission from lung-infected patients and from contaminated dust of homes
Prolonged contact is required – the bacterium is not strongly infectious
(Also M. bovis from infected cows via unpasteurised milk)
Disease Incubation and Within weeks or months, typically in the lungs of patients already vulnerable due to
parameters venue malnutrition or inferior health
Signs, A persistent cough, producing sputum (phlegm), with fatigue, loss of appetite, weight
symptoms loss and fever
and diagnosis Confirmation by a skin test, a chest X-ray and bacteriological test of sputum
Treatment A combination of antibiotics, particularly isoniazid and rifampicin, for at least 6 months
Prognosis Improvement within 2–3 weeks of early diagnosis and treatment, full recovery in 6–12
months
An ignored infection that spreads to other organs is likely to be fatal
For patients with HIV/AIDS, TB is likely to be the cause of death
Prevention and BCG vaccination often protects younger people and is typically given to children and
control young adults at risk
WHO Distribution Worldwide; strains resistant to anti-TB drugs have emerged in all countries
status Global About 10 million in 2018 for 1.5 million of whom the condition was fatal
incidence and Within the UK there are over 5400 cases per year, most non-UK born, from Sub-Saharan
mortality Africa (37%) and South Asia (47%)
▲ Table 10.5 Tuberculosis – the profile
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HIV/AIDS
10 Auto-immune deficiency syndrome (AIDS) is a disease caused by the human
immunodeficiency virus (HIV, Figure 10.15). Viruses are disease-causing agents, rather
than ‘organisms’.
Infection with HIV is only possible through
glycoprotein contact with blood or body fluids of infected
lipid
people, such as may occur during sexual
membrane intercourse, sharing of hypodermic needles
by intravenous drug users, and during
RNA
Antibiotics are not pregnancy, labour, delivery and breast
reverse
effective against transcriptase feeding of a newborn baby. Also, blood
viruses. What (enzyme) transfusions and organ transplants will
antibiotics are and why transmit HIV but donors are now screened
protease
this is so is explained on (enzyme) for HIV infection in most countries. HIV is
pages 216–21. not transferred by contact with saliva on a
capsid
(protein)
drinking glass, nor by sharing a towel, for
▲ Figure 10.15 The structure of the human example. Nor does the female mosquito
immunodeficiency virus (HIV) transmit HIV when feeding on human blood.
The spread of HIV and the eventual onset of AIDS in patients are outpacing the current
efforts of scientists and doctors to prevent them. The WHO records the current state of
this pandemic (Figure 10.16).
T-lymphocytes (CD4 helper cells) and the development of AIDS

T-lymphocytes are a particular type of white blood cell (page 172). An antigen is,
normally, a protein that is recognised by the body as foreign (non-self, see page 225)
and that stimulates an immune response (page 236). HIV attacks T-lymphocytes.
Estimated number of adults and children newly infected with HIV during 2018 – total: 1.7 million
Europe
170 000
Eastern Mediterranean
41 000
Americas South-East Asia
160 000 Africa 170 000
1.1 million Western Pacific
120 000
End-2018 global estimates

(adults and children)
• People living with
HIV/AIDS ………........ 37.9 million
• New HIV infections
in 2018 ……………... 1.7 million
• Deaths due to HIV/AIDS
in 2018.......………... 770 000
• Cumulative number of deaths
due to HIV/AIDS ….....nearly 32 million
▲ Figure 10.16 HIV/AIDs – global estimates (WHO data)

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HIV particle
HIV antigens
10
T-lymphocyte
remain on
surface of
infected cell
1 binding protein
on virus capsule
CD4 receptor

3
2
binding leads
to fusion of
capsule with
cell surface virus core enters
membrane lymphocyte
▲ Figure 10.17 HIV infection of a white blood cell
HIV is one of a minority of viruses that has an additional external envelope – a

membrane of lipids and proteins. (This membrane is actually ‘borrowed’ from the last
cell that it infected.) Once in the bloodstream, specific proteins on the outer membrane
of the virus are antigens. These proteins attach the virus to protein receptors of the
surface of T-lymphocytes (CD4 helper cells of the immune system, page 227) and the
core of the virus penetrates to the cytoplasm (Figure 10.17).
HIV is a virus belonging to a group known as retroviruses. Retroviruses are RNA
viruses with a unique ‘infection process’. On entering the cytoplasm of a host cell the
virus RNA is translated into DNA which then attaches to that of a chromosome in the
host’s nucleus (Figure 10.18). The steps to this are as follows.
Inside the lymphocyte, the RNA strands and an enzyme called reverse transcriptase are
released from the core of the virus. Then, using the viral RNA as the template, a DNA
copy is formed by the action of the reverse transcriptase. (Remember, RNA is single
stranded but DNA is a double-stranded molecule, page 123).
This DNA enters the nucleus of the lymphocyte and attaches itself to a chromosome.
It becomes a permanent part of the host cell’s genome. It is known as a provirus. After
an initial, mild form of AIDS (a brief ’flu-like illness within a few weeks, or possibly
the development of a rash or swollen glands) the provirus remains dormant (called the
latency period).
However, at some later time the viral DNA replicates, leading
1 RNA strands
to the production of new viruses which then invade and kill
other lymphocytes (Figure 10.19, overleaf). It is not clear
2 DNA copy formed
by action of whether infected T-lymphocytes are killed by the virus
reverse transcriptase they harbour or by the actions of the patient’s immune
3 RNA strand removed system against these infected cells. However, AIDS-related
by action of symptoms follow, caused by pathogens that are around us all
ribonuclease
the time. These are normally resisted by a healthy immune
4 transcription of
complementary
system but, without it, the body cannot effectively resist
DNA strand by action (Figure 10.20, overleaf). We say the patient has now become
of DNA polymerase
immunocompromised.
5 DNA double strand
integrated into
DNA of a chromosome
in nucleus of host
–provirus
(latent virus)
▲ Figure 10.18 How HIV becomes part of the white

blood cell’s genome
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SEM of a white cell from which HIV capsules are budding off
10
opportunistic infection
(e.g. pneumonia)
takes over – patient’s

immune system now
hopelessly compromised
early
symptoms
initial
infection
viral proteins and RNA being synthesised and new HIV ‘cores’
assembled then budded off with part of the host cell surface 1200
membrane as the capsules Key death
CD4 helper T-cells per mm3
the ‘budding’ process of blood
1000
normal HIV RNA copies per mm3
range for of blood 1500
T-lymphocyte
800
RNA core
formed
viral 600 1000
proteins
cell surface formed
membrane signifcantly
becomes the depressed 400
virus capsule messenger T-lymphocytes
RNA copy 500
to ribosomes
200
severe T-lymphocyte
genes of
depletion
HIV on host
copy of chromosome 0 0
0 3 6 9 1 2 3 4 5 6 7 8 9 10
viral RNA
weeks years
▲ Figure 10.19 Activation of the HIV genome and the ▲ Figure 10.20 The profile of an AIDS infection
production of new HIV
Social, economic and biological factors in the prevention and control of

HIV/AIDS
AIDS is difficult to treat because viruses are not controlled by antibiotics. AIDS patients
Question are offered drugs that slow down the progress of the infection. The three most popular
5 Suggest what drugs (AZT and two protease inhibitors) interrupt the reverse transcription of nucleic
features of HIV and acid. A combination of drugs is used to prevent HIV from rapidly developing resistance
the disease it causes to any one drug. This also helps to avoid dangerous or unpleasant side effects that some
create particular patients experience.
problems for the However, there is no cure for HIV/AIDS. Ideally, a vaccine against HIV would be the
people and the best solution – one designed to wipe out infected T-lymphocytes and free virus particles
economies of less- in the patient’s bloodstream. The work of several laboratories is dedicated to this
developed countries
solution. The problem is that infected T4 cells in the latent state frequently change the
such as Zimbabwe or
membrane marker proteins they carry due to the HIV genome within. Effectively, HIV
Zambia?
can hide from the body’s immune response by frequently changing its identity.
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Current effective measures to prevent the spread of HIV include male circumcision.
Recent studies have shown that the incidence of AIDS is significantly higher in
uncircumcised males. Circumcised males were seven times less likely to transmit to or
receive HIV from their partner. The reason for this is that the mucous membrane of the
10
inner surface of the foreskin has cells with receptors that HIV can exploit. Consequently,
it is possible that infection of future generations with HIV might be reduced if male
circumcision was practised more widely. However, if this were to encourage males to
participate in unsafe sex with numerous partners, it would defeat the object.
Factors Prevention Control

Social Effective education programmes so that the Contact tracing, where a person diagnosed as HIV-
vulnerable understand the cause and effects of HIV positive is willing and able to identify those who
infection, and the best steps to remain healthy, have been put at risk by contact
whether or not they are literate
Encouraging faithfulness to one partner
Economic Condoms being made freely available to the sexually Funding of testing of the sexually-active population
active population to identify HIV-positive people (if people will accept
Sterile needles being made freely available to this invasion of their privacy)
intravenous drug users Funding and supply of the drugs that prevent the
replication of the virus inside host cells
Biological The practice of ‘safe sex’ by the use of condoms to Drug therapy
prevent the transmission through infected blood or Research on the development of a vaccine
semen
Replacement of breast feeding by bottle feeding of
Screening of blood donors for HIV, so that infected infants of HIV-positive mothers, and other WHO
blood is not taken and used strategies for helping HIV-infected mothers
▲ Table 10.6 The prevention and control of HIV/AIDS
Pathogen Pathogen A single-stranded RNA retrovirus, human immunodeficiency virus (HIV)

taxonomy
Transmission Contact with blood or body fluids of infected people, via sexual intercourse, the sharing
of hypodermic needles by intravenous drug users or during breast feeding of infants
Disease Incubation and Once in the blood, the virus immediately enters T-lymphocytes (CD4 cells) – components
parameters venue of the immune system
Signs, Early symptoms typical of mild ’flu occur in a few weeks
symptoms and Presence of HIV can only be confirmed by HIV blood test
diagnosis
The patient’s terminal vulnerability to any opportunistic infections typically delayed
months or years
Treatment A combination of drugs that interrupt reverse transcription of nucleic acid (AZT and two
protease inhibitors)
Prognosis There is no cure for HIV/AIDS but an effective vaccine is sought
Patients ultimately succumb to other infection, e.g. TB or measles
Prevention and Safe sex using condoms
control Needle exchange schemes for intravenous drug users
Male circumcision
WHO status Distribution Worldwide, after the first cases of the disease came to light in the 1980s in the USA
Global Estimated total of newly infected individuals was 1.7 million in 2018 two-thirds are in
incidence and Africa
mortality Estimated annual death rate was 770 000 in 2018
▲ Table 10.7 HIV/AIDS – the profile
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10.2 Antibiotics
10 Learning outcomes
10.2.1 outline how penicillin acts on bacteria and why antibiotics do not affect
viruses
10.2.2 discuss the consequences of antibiotic resistance and the steps that can
be taken to reduce its impact
Starting point
★ The ‘age of antibiotics’ began in the 1940s with the availability of penicillin.
With an increase in antibiotic resistance is this age about to come to an end?
Introducing antibiotics
Antibiotics were discovered relatively recently – with a chance observation in 1928.
By the 1950s, it became possible to treat patients with courses of antibiotics that cured
many bacterial infections. More recently, the excessive use of antibiotics has generated
problems, as we shall see later.
Antibiotics are naturally occurring chemical substances obtained mainly from certain
fungi and bacteria commonly found in the soil. When antibiotics are present in low
concentrations they inhibit the growth of other microorganisms or cause their outright
death, as demonstrated in Figure 10.21.
The discovery, isolation and development of the first antibiotic, penicillin, was not an easy
task. (It took from 1929 until 1944.) Since then, over four hundred different antibiotics have
been isolated and tested. Of these, only about 50 have proved to be non-toxic to patients.
These antibiotics have achieved wide usage. Those effective against a wide range of pathogenic
bacteria are called broad-spectrum antibiotics. These include chloramphenicol. Others,
including streptomycin, are effective against a limited range of bacteria.
To a known species of bacteria

growing on nutrient agar was
added a mast ring with each ‘arm’
impregnated with a different
antibiotic (colour coded). Then CM
the plate was closed and
incubated. From the result
M
T
S T RI N G
PI
MA
S
(opposite) there is evidence

that growth of this bacterium
is more sensitive to certain
antibiotics (e.g. CM, A)
than to others (e.g. S, I ).
PC
known species of
bacteria growing
on nutrient A
I
medium
region where
C
bacteria
have been killed
Different antibiotics are contained in the arms of the
mast ring, so that sensitivity to many antibiotics may be
tested simultaneously.
▲ Figure 10.21 Investigating sensitivity to antibiotics
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How antibiotics work
Antibiotics work by disrupting the metabolism of prokaryotic cells. It is in these
division and growth phases that bacteria are vulnerable to antibiotic action – an effective 10
antibiotic specifically disrupts one of three major aspects of the growth or metabolism
of bacteria. Since the particular components, metabolites or enzymes concerned are not
found in eukaryotic cells in the same form, the antibiotic is not toxic to the mammalian
host tissues.
1 Cell wall synthesis inhibition
10.2 Antibiotics
The most effective antibiotics work by interfering with the synthesis of bacteria’s cell
walls. Once the cell wall is destroyed, the delicate plasma membrane of the bacterium
is exposed to the destructive force generated by excess uptake of water by osmosis, and
possibly, as well, to attack by antibodies and phagocytic macrophages.
Several antibiotics, including penicillin, ampicillin, and bacitracin, bind to and
inactivate specific wall-building enzymes. These are the enzymes required to make
essential cross-links between the linear polymers of the walls in particular species.
In the presence of the antibiotic, wall polymers continue to be synthesised by the
pathogens, but the individual strands are not linked and bound together. The walls fall
apart.
2 Protein synthesis inhibition

Other antibiotics inhibit protein synthesis by binding with ribosomal RNA. The
ribosomes of prokaryotes (known as 70S) are made of particular RNA subunits,
together with many polypeptides (which mainly function as enzymes). The ribosomes
of eukaryotic cells are larger (80S), and are built with different RNA molecules and
polypeptides. Antibiotics like streptomycin, chloramphenicol, tetracyclines and
erythromycin all bind to prokaryotic ribosomal RNA subunits unique to bacteria. Here
their presence causes protein synthesis to be terminated.
3 Nucleic acid synthesis

A few antibiotics interfere with DNA replication or transcription, or they block mRNA
synthesis. These antibiotics, for example the quinolones, are not as selectively toxic as
other antibiotics. This is because the processes of replication and transcription do not
differ so greatly between prokaryotes and eukaryotes as wall synthesis and protein
synthesis do.
Why antibiotics do not affect viruses

We have seen that viruses are non-living particles (page 27). A virus lacks cell structure
and has no metabolism of its own to be interfered with or disrupted. Instead, viruses
reproduce using metabolic pathways in their host cell that are not affected by antibiotics.
Antibiotics cannot be used to prevent viral diseases.
How bacteria become resistant to antibiotics

Before antibiotics became available to treat bacterial infections the typical hospital
ward was filled with patients with pneumonia, typhoid fever, tuberculosis, meningitis,
syphilis and rheumatic fever, for example. These diseases, all caused by bacteria,
claimed many lives, sometimes very quickly. The discovery of antibiotics brought a
significant change. Patients with bacterial infections were treated with an antibiotic, and
quickly overcame their infection. In fact, antibiotics have been very widely used – to
great success.
However, in any large population of a species of pathogenic bacteria, some of the
bacteria may acquire or carry a gene for resistance to the antibiotic in question.
Sometimes this gene has arisen by a spontaneous mutation. Sometimes the gene has
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Key after treatment with antibiotic
with resistance gene the bacteria with antibiotic
10
without resistance gene resistance have a selective
100 advantage and now make up 100
the majority of the population
% population growing in
80 80
% population growing
absence of antibiotic
with antibiotic
60 60
40 40
20 20
0 0
▲ Figure 10.22 Development of antibiotic resistance in bacteria
been acquired through bacterial conjugation between bacteria of different populations,

or when the bacterium itself has been parasitised by a virus that brought the resistance
gene within its nucleic acid (Figure 10.22).
Bacterial conjugation is not a form of reproduction. Bacteria reproduce asexually
through binary fission, but they are able to share genes – for example, for antibiotic
resistance – by copying them and passing on the genetic material via a pilus.
When an individual bacterium has acquired resistance it confers no selective advantage
at all in the absence of the antibiotic. The resistant bacterium must compete for resources
with non-resistant bacteria. However, when an antibiotic is administered, most bacteria
of the population are killed off. Only at this stage will the bacteria with resistance to
the antibiotic flourish, and then come to create the future population, all of which
now carry the gene for resistance to the antibiotic. At this point, the genome has been
changed abruptly, and the future effectiveness of that antibiotic is compromised.
Today, the issue of bacterial resistance to antibiotics in healthcare has become a major
problem. As pathogenic bacteria developed genes for resistance to antibiotic actions,
different antibiotics were used in response. The inevitable outcome of this is that
pathogenic bacteria slowly acquire multiple resistance (Figure 10.23). For example, a
strain of Staphylococcus aureus has acquired resistance to a range of antibiotics including
methicillin. Now, so-called methicillin-resistant Staphylococcus aureus (MRSA) is referred
to as a ‘hospital superbug’ because of the harm its presence has inflicted in these places.
(Actually, ‘superbugs’ are found everywhere in the community, not just in hospitals.)
MRSA poses the greatest threat to patients who have undergone surgery. With cases of
MRSA to treat, the intravenous antibiotic called vanomycin is prescribed, but recently
there have been cases of partial resistance to this drug, too (Figure 10.24).
Similarly, a strain of the bacterium Clostridium difficile is now resistant to all but two
antibiotics. This bacterium is a natural component of our gut ‘microflora’. It is only
when C. difficile’s activities are no longer suppressed by the surrounding, huge, beneficial
(i.e. ‘friendly’) gut flora that it may multiply to life-threatening numbers and then may
trigger toxic damage to the colon.
Suppression of beneficial gut bacteria is a typical consequence of heavy doses of broad-
spectrum antibiotics, administered to overcome infections by superbugs.
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pathogenic bacteria
cell carries gene for resistance
to an antibiotic (bacterium
able to inactivate antibiotic) antibiotic-resistant gene acquired
by mutation
10
or
by conjugation with a bacterial
cell that carries the gene
or
when infected by a virus
(phage) that has picked up
pathogen invades and triggers disease the gene in another host
in human (or in a pet or farm animals)
10.2 Antibiotics
treated with antibiotic e.g. penicillin
most bacterial cells perish
but
antibiotic-resistant cell survives
gives rise to a new population of

antibiotic-resistant bacteria
Question (non-resistant competitor
bacteria have been killed,
so there is no competition
6 Explain: for resources)
a why doctors
ask patients process is repeated in another %
to ensure that antibiotic-treated host
40
(following another infection
they complete and treatment with a different
their course of antibiotic e.g. methicillin) 30
antibiotics fully causing multiple-antibiotic-
resistant bacteria to evolve
b why the medical 20
profession tries to
combat resistance 10
by regularly
alternating the overuse and misuse of antibiotics create the 0
perfect breeding ground for resistant bacteria 1992 1994 1996 1998 2000
type of antibiotic
development of multiple-resistant
used against an In the long term, the drugs industry faces
Staphylococcus aureus, 1992–2001
infection. the challenge of producing new antibiotics
(% of infected samples received in pathology labs)
faster than antibiotic-resistant bacteria evolve.
▲ Figure 10.23 Multiple antibiotic resistance in bacteria
50
sent to labs in England and Wales
Staphylococcus aureus samples
that are methicillin resistant/%
40
30
20
10
0
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001
year
▲ Figure 10.24 The increasing incidence of MRSA
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10
▲ Figure 10.25 False-colour SEMs of Staphylococcus aureus (×10 000) and Clostridium difficile (×10 000)
THE TIMES I Thursday May 1 2014
Antibiotics crisis means scratch could kill
Common infections will once again kill scratches and common infections could
as the rise of antibiotic-resistant super- all become fatal, the report warns.
bugs has a “devastating” effect on Doctors said the problem demanded
modern medicine, the World Health an international effort modelled on the
Organisation said yesterday. fight against Aids, including a clampdown
Resistance to commonly used drugs is on the use of antibiotics, the end of their
increasing across the planet and is now use in agriculture and the urgent
a problem that could affect “anyone, development of new drugs. Patients
of any age, in any country”, the WHO must only use antibiotics prescribed by
said in a report tracking the rise of super- a doctor and complete a full course even
bugs in 114 countries. if they are feeling better, the WHO said.
Patients are already suffering because
those infected by superbugs are twice as
likely to die as those with non-resistant Chris Smyth Health Correspondent
infections. Routine operations, minor
21 The consequences of antibiotic resistance

number of antibiotic drugs approved
18 19 A natural response to this challenging situation is to search

15 for new and more effective antibiotics to replace those that
have become ineffective. This has been the response of
12
pharmaceutical firms – and continues to be so. However, this is
11 11 11
9 proving increasingly difficult – the number of new antibiotics
6 being developed each year has fallen dramatically (Figure 10.26).
Pathogens tend to develop resistance faster than new antibiotics
3 4
3 1 can be found.
0
1980– 1985– 1990– 1995– 2000– 2005– 2010–
1984 1989 1994 1999 2004 2009 2014
year intervals
▲ Figure 10.26 The number of new antibiotics
developed and approved in the past three
decades
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In this situation the strategy to combat the problem includes:
» Prudent antibiotic use.
Avoidance of the unnecessary and inappropriate exposure of microorganisms to
antibiotics in medical clinics, veterinary clinics, animal husbandry and agriculture.
10
These drugs must be used sparingly, and only in situations where there is no
alternative appropriate treatment. When a course of antibiotics is prescribed,
the antibiotics should be taken to completion, and not abandoned as soon as the
patient feels some improvement. The widespread prophylactic use of antibiotics in
animal husbandry should be minimalised and preferably discontinued. Animals
reared intensively have been fed antibiotics as a component of their diet, following
10.2 Antibiotics
Question
the discovery that they grew faster and reached marketable weights more quickly.
7 Antibiotics are However, antibiotic residues have accumulated in the food chain, and many more
widely used as bacteria have been exposed to situations where resistance may evolve and emerge.
prophylactics in » Surveillance.
animal husbandry. The monitoring of the appearance of new cases of resistance to antibiotics, and
What does this prompt circulation of the data to healthcare professionals and institutions.
mean, why does this » Infection control.
happen, and what A renewed focus on the reduction in the spread of infection in general, so that the
possible dangers need for the use of antibiotics is reduced – on the principle that prevention is better
arise from this use of than cure.
antibiotics?
Animals get George gets

antibiotics and antibiotics and
develop resistant develops resistant
bacteria in their guts. bacteria in his gut.
Drug-resistant
bacteria can
remain on meat George stays at
from animals. home and in the
When not handled general community.
or cooked properly, Spreads resistant
the bacteria can bacteria.
spread to humans.
George gets care
at a hospital.
Fertiliser or water Resistant germs spread

containing animal faeces directly to other patients or
and drug-resistant bacteria indirectly on unclean hands
is used on food crops. of healthcare providers.
Hospital
Resistant bacteria
Drug resistant bacteria spread to other
in the animal faeces can patients from the
remain on crops and be surfaces within
eaten. These bacteria can the hospital.
Vegetable farm
remain in the human gut.
Patients go home
▲ Figure 10.27 How antibiotic resistance spreads
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SUMMARY
10 » Health is a state of physical, mental and social glucose and salts is essential once the disease is
well-being, not merely the absence of disease. diagnosed. About 50 per cent of untreated cases
Diseases caused by disease-causing agents are are fatal.
infectious diseases since they may be transferred. » The TB bacterium is transmitted by droplets from
Non-infectious diseases, such as lung cancer and infected lungs during persistent coughing. In the
sickle cell anaemia, are not ‘caught’ from other lungs of people weakened by malnutrition or ill-
organisms. health the bacterium overcomes resistance and
» Viruses consist of DNA or RNA, wrapped in a attacks the alveoli. Prolonged treatment with a
protein coat. Viruses take over host cells and combination of antibiotics leads to recovery but,
convert the cellular machinery to produce more untreated, TB will attack other body systems and
viruses which escape and may repeat the process. cause death. A vaccine is available and is given to
Human viral diseases include HIV/AIDS, measles people in some countries, particularly children,
and smallpox. but how effective the vaccine is varies according
» HIV is transmitted by contact with blood or body to geography. Distribution of the disease is
fluids. It enters lymphocytes of the immune worldwide but it is a particular threat to HIV/AIDS
system and ultimately destroys them and the patients. Strains resistant to anti-TB drugs have
body’s resistance to other diseases. Treatment emerged in all countries.
with drugs that interfere with the replication » Diseases caused by eukaryotic organisms
of the virus delays the onset of AIDS but there include malaria, due to the protoctist Plasmodium,
is no vaccine as yet and therefore no cure. transferred by the mosquito. The life cycle of
Transmission may be controlled by barrier Plasmodium is acted out in the liver and red blood
methods of contraception but HIV/AIDS especially cells and results in periodic release of toxins
harms societies when young, economically active and high fever. Protection from mosquito bites is
members and their children are infected. critical but a combination of anti-malarial drugs
» Bacterial diseases are caused by pathogenic permits a patient with malaria to improve within
bacteria. They are vulnerable to antibiotics, unlike 48 hours. Malaria is endemic in tropical and sub-
viruses. Examples of bacterial diseases include tropical regions and kills thousands of children
cholera and tuberculosis (TB) but most bacteria in remote areas of sub-Saharan Africa. A well-
are not disease-causing at all. funded drive to find a vaccine continues.
» The cholera bacterium is principally transmitted » Antibiotics are developed from naturally-
in water or foods contaminated by human faeces. occurring chemicals obtained from certain
The bacterium releases a toxin that triggers the bacteria and fungi and that inhibit the growth of
loss of water and salts from the intestines, causing other microorganisms. They work by destroying
diarrhoea and severe dehydration. Cholera the pathogenic bacteria or by interfering in their
has been eradicated where there is effective metabolism so that the body’s own defences
processing of sewage and the purification of can work effectively. Unfortunately, pathogens
drinking water. Vaccines are available but prompt develop resistance so new antibiotics are
treatment by rehydration with a dilute solution of constantly sought.

1 The main cause of tuberculosis (TB) in humans is the bacterium Mycobacterium
tuberculosis.
Most cases of the disease involve the lungs. The bacterium can enter cells and
remain inactive in a latent (dormant) state. However, the bacterium can become
active to produce symptoms of the disease.
a TB in humans can be caused by another species of bacterium, M. bovis.
State the mode of transmission of this pathogen to humans. [1]
b The standard treatment for TB continues for six months and initially involves
the use of four different antibiotics.
If no antibiotic resistance is detected, the treatment is reduced to two of the
four antibiotics. The two antibiotics used are rifampicin and isoniazid.
Suggest the benefits of beginning the treatment with four different
antibiotics. [2]
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c Multidrug-resistant TB (MDR-TB) occurs if resistance develops to rifampicin
and isoniazid.
The treatment for MDR-TB can last up to 30 months and involves different 10
antibiotics to the standard treatment.
Table 1.1 shows the number of reported cases of TB and MDR-TB in the South-
East Asia region between 2005 and 2014, as published by the World Health
Organization (WHO).
year total number of reported total number of reported

cases of TB cases of MDR-TB

2005 1 947 603 68
2006 2 104 673 779
2007 2 202 149 918
2008 2 287 803 1 717
2009 2 328 230 2 560
2010 2 332 779 4 263
2011 2 358 127 6 615
2012 2 331 455 14 957
2013 2 297 033 18 384
2014 2 580 605 17 386
▲ Table 1.1
State the trends shown in Table 1.1. [2]
d TB is a disease of global importance.
Discuss the factors influencing the trends shown in Table 1.1. [3]
[Total: 8]
(Cambridge International AS and A Level Biology 9700 Paper 22 Q2 d, e, f, g Feb/Mar 2018)
2 a Moves to prevent the spread of infectious disease within a local community
have included:
A an improved supply of water, including sewage treatment
B insect control
C milk pasteurisation.
For each of these preventative measures, describe a disease they are
effective against and explain why. [12]
b What features of the lifecylce of the pathogen that causes malaria make the
development of an effective vaccine especially difficult? [4]
c Explain why malaria is endemic in tropical and sub-tropical regions but absent
or rare elsewhere in the world. [2]
d What is the significant difference between a disease outbreak which is
classified as an epidemic and as a pandemic? [2]
[Total: 20]
3 a The human immunodeficiency virus (HIV) is a retrovirus that is responsible for
the disease of AIDs. Explain what ‘retrovirus’ means.
b With the onset of AIDs, the immune system is said to be ‘hopelessly
compromised’. Explain this, and outline how HIV brings this about.
c Ideally, a vaccine is sought against HIV. Why is the development of an effective
vaccine proving difficult in this case?
4 a Explain the mechanism by which antibiotics may be effective against
pathogenic bacteria but that results in them having no effect on viruses.
b Antibiotics have been thought of as ‘wonder drugs’ but today are used
selectively and sometimes with restraint. What are the reasons for this change
in attitudes and practice?
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AS LEVEL
11 Immunity
11 Immunity
An understanding of the Learning outcomes

immune system shows how
cells and molecules function By the end of this topic, you will be able to:
together to protect the 11.1.1 describe the mode of action of phagocytes (macrophages and neutrophils)
body against infectious 11.1.2 explain what is meant by an antigen (see 4.1.3) and state the difference
diseases and how, after an between self antigens and non-self antigens
initial infection, the body is 11.1.3 describe the sequence of events that occurs during a primary immune
protected from subsequent
response with reference to the roles of: macrophages; B-lymphocytes,
infections by the same
pathogen. Phagocytosis is
including plasma cells; T-lymphocytes, limited to T-helper cells and
a more immediate non- T-killer cells
specific part of the immune 11.1.4 explain the role of memory cells in the secondary immune response and
system, while the actions in long-term immunity
of lymphocytes provide
effective defence against
specific pathogens.
Starting point
★ The immune system has non-specific and specific responses to pathogens.
Auto-immune diseases are the result of failures in the system to distinguish
between self and non-self.
11.1 The immune system

Responses to infection
Pathogens do not gain easy entry to the body because:
» externally, the keratinised protein of the dead cells of the epidermis are tough and
impervious unless broken, cut or deeply scratched
» internal surfaces, in particular the trachea, bronchi and the bronchioles of the
breathing apparatus, and the gut are all lined by moist epithelial tissue. These
internal barriers are protected by mucus, by the actions of cilia removing the mucus,
and some by digestive enzymes or strong acid (as in the stomach).
However, these barriers are sometimes crossed by pathogens. In response, there
are internal ‘lines of defence’. If a blood vessel is ruptured then the blood clotting
mechanism is activated. In the blood and tissue fluid, the immune system is triggered,
which is covered in more detail shortly.
Action of phagocytes – macrophages and neutrophils

The initial response to tissue damage is that the volume of blood in the damaged
area increases, and white blood cells and plasma accumulate outside the enlarged
capillaries.
The white blood cells fall into two functional groupings depending on their roles in the
defence against disease.
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stem cells in the bone marrow General phagocytic white cells engulf ‘foreign’ material. These are the
neutrophils and the macrophages. Neutrophils make up 60 per cent of
all white blood cells in the blood, but they are short-lived. Macrophages
are the principal ‘rubbish-collecting cells’ found throughout the body
11
cells migrate to the lymph nodes
tissues (Figure 11.1). These responses to infection destroy any invading
short-lived pathogen.
phagocytic cells
Other white blood cells called lymphocytes, produce the antibody
neutrophils of the
blood circulation:
reaction to infection or invasion of foreign matter. This, the immune
make up 60% of all response, is triggered by and directed towards specific pathogens.

white cells
highly efficient at engulfing
You can see some phagocytic white cells and a lymphocyte in the
bacteria either in blood or photomicrograph of a blood smear in Figure 8.6. You will probably
in tissue fluids outside the have already seen them in a prepared microscope slide of mammalian
capillaries long-lived
survive only a few days phagocytic cells blood. Figure 11.3 (overleaf) also shows a white blood cell engulfing a
monocytes that
bacterium.
replenish the The blood also delivers special proteins (complement proteins), which
macrophages
are activated by the presence of infection (Figure 11.2). Complement
macrophages:
the principle ‘rubbish-collecting’
proteins enhance the work of white blood cells in overcoming
cells of the body infections. Some trigger the lysis of invading microorganisms, and
leave the blood circulation and lie others, the opsonins, bind to pathogenic bacteria and so increase
in wait in the liver, kidneys, spleen phagocytosis.
and lungs
always ready to respond to debris Cells infected with viruses produce proteins called interferons. These
and invading cells
bind to neighbouring, healthy cells and trigger synthesis of antiviral
▲ Figure 11.1 The phagocytic cells of the proteins. Viral replication is halted.
body’s defence mechanism
The above responses to infection are referred to as non-specific
responses because they help to destroy any invading pathogen. By
contrast, the immune response we discuss next is triggered by and
directed towards specific pathogens.
The immune response

The immune response is our main defence once invasion of the body
opsonins (antibodies or by harmful microorganisms or ‘foreign’ materials has occurred. It is
complement proteins) neutrophil moves
attach to bacterium) towards bacterium
particular leucocytes (white blood cells) called lymphocytes that are
responsible for the immune response. They make up 20 per cent of the
leucocytes circulating in the blood plasma (or found in the tissue fluid –
remember, white blood cells also move freely through the walls of blood
phagosome vessels).
formed by
pseudopodia Lymphocytes detect any ‘foreign’ matter entering from outside our bodies,
including macromolecules as well as microorganisms, as different from
lysosome fuses
with phagosome
out body cells and our own proteins. Any molecule the body recognises as
and releases a foreign or non-self substance is known as an antigen.
hydrolytic enzymes
What recognition of ‘self’ entails
All cells are identified by specific molecules – markers, if you like – that
digestion of bacterial are lodged in the outermost surface of the cell. In fact, these molecules
cell and absorption of include the highly variable glycoproteins on the cell surface membrane.
products into neutrophil
Remember, glycoproteins occur attached to proteins there. Look at
▲ Figure 11.2 Phagocytosis by a white Figure 4.3, page 83 and remind yourself of the ‘fluid mosaic’ structure of
cell – a neutrophil this membrane.
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11
11 Immunity
white cell engulfing

bacterium
red cells
▲ Figure 11.3 Photomicrograph of a white blood cell engulfing a bacterium (×7500)
The glycoproteins that identify cells are also known as the major histocompatibility
complex antigens – but we can refer to the major histocompatibility complex as MHC
from now on. There are genes on one of our chromosomes (chromosome 6, actually) that
code for MHC antigens. Each individual organism’s MHC is genetically determined – it
is a feature we inherit. As with all inherited characteristics that are products of sexual
reproduction, variation occurs. So each of us has distinctive MHC antigens present on
the cell surface membrane of most of our body cells. Unless you have an identical twin,
your MHC antigens are unique.
Lymphocytes of our immune system have antigen receptors that recognise our own MHC
antigens and can tell them apart from any ‘foreign’ antigens detected in the body. After all,
it is critically important that our own cells are not attacked by our immune system.
Lymphocytes and the antigen–antibody reaction

We have two distinct types of lymphocytes (Figure 11.4), based on the ways they
function. Both cell types originate in the bone marrow where they are formed from stem
cells. As they mature they undergo different development processes in preparation for
their distinctive roles.
» B-lymphocytes secrete antibodies.
» T-lymphocytes, some of which assist B-lymphocytes (T-helper cells), and others which
may attack infected cells (T-killer cells). Activated T-killer cells bind to the specific
antigen presenting cells of virus infected cells or cancerous cells. After binding they
release enzymes that break open the cell surface membrane, killing the cell.
Question 1 Explain the significance of the role of the thymus gland in destroying T-lymphocytes
that would otherwise react to body proteins.
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How do these distinctive roles develop?
T-cells leave the bone marrow early during development and they undergo
differentiation in the thymus gland. Here they mature. The thymus gland is found in 11
the chest, just below the breast bone (sternum). It is an active and enlarged gland from
birth to puberty. The gland then shrinks in size, its task completed.
It is while T-lymphocytes are present in the thymus gland that the body selects out
all the lymphocytes that would otherwise react to the body’s own cells. The surviving
T-lymphocytes then circulate in the plasma and are stored in lymph nodes.

The T-lymphocytes do not secrete antibodies. The role of T-lymphocytes is cell-
mediated immunity – meaning their role in the immune response does not directly
involve antibodies, although some have a role in the activation of B-lymphocytes, as
we shall see shortly.
B-lymphocytes complete their maturation in the bone marrow, prior to circulating in
the blood and being stored in lymph nodes. The role of the majority of B-lymphocytes,
after recognition and binding to a specific antigen, is to proliferate into cells (called
plasma cells) that secrete antibodies into the blood system. This is known as humoral
immunity.
Now while both T- and B-cells have molecules on the outer surface of their cell surface
membrane that enable them to recognise antigens, each T- and B-lymphocyte has only
one type of surface receptor. Consequently, each lymphocyte can recognise only one
type of antigen.
repeated
cell division
(mitosis)
stem cell of cell matures T-cell migration

bone marrow into lymphocyte during maturation
thymus gland where
T- lymphocytes that
react to body’s own
cells are weeded out
B-cell matures in
bone marrow mature lymphocytes lymph nodes occur
circulate in the blood all over the body but
system, escape into are concentrated in
the tissue fluid neck, arm pits and
surrounding body cells, groin
and collect in the lymph
system; many are stored
in lymph nodes
B-lymphocyte awaits chance T-lymphocyte awaits chance

encounter with an antigen encounter with an antigen
▲ Figure 11.4 T- and B-lymphocytes
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How do B- and T-lymphocytes respond to an infection?
11 When an infection occurs the leucocyte population increases enormously and many
collect at the site of the invasion. The complex response to infection is begun. The
special roles of T- and B-lymphocytes in this response are given below.
Refer to Figure 11.6 as you follow these steps.
1 On the arrival of a specific antigen in the body, B-lymphocytes with surface
receptors (antibodies) that recognise that particular antigen, bind to it.
Antibodies initially occur attached to the cell surface membrane of B-lymphocytes but
11 Immunity
later are also mass produced and secreted by cells derived from the B-lymphocyte, but
only after that B-lymphocyte has undergone an activation step (step 4, below).
antigen
antibodies occur
attached to cell
surface membrane
of B-lymphocytes
and
Figure 11.5 The structure of
an antibody may be secreted by exocytosis as
free-standing molecules
2 On binding to the B-lymphocyte, the antigen is taken into the cytoplasm

by endocytosis, before being expressed on the cell surface membrane of the
B-lymphocyte.
3 Meanwhile, T-lymphocytes can only respond to antigens when presented on the
surface of other cells. Phagocytic cells of the body, including macrophages, engulf
antigens they encounter. This may occur in the plasma, lymph or tissue fluid. Once
these antigens are taken up, the macrophage presents them externally by attaching
the antigen to their surface membrane proteins, MHC antigens. This is called
antigen presentation by a macrophage.
4 T-cells come in contact with these macrophages and briefly bind to them. The
T-lymphocyte is immediately activated. They become T-helper cells.
5 T-helper now bind to B-lymphocytes with the same antigen expressed on their cell
surface membrane (step 2 above). The B-lymphocyte is activated by the binding of
this chemical. It is now an activated B-lymphocyte.
6 Activated B-lymphocytes immediately divide very rapidly by mitosis forming a
clone of cells called plasma cells. Plasma cells are packed with rough endoplasmic
reticulum (RER). It is in these organelles that the antibody is mass produced. The
antibody is then exported from the plasma cell by exocytosis. The antibodies are
normally produced in such numbers that the antigen is overcome. The production of
an activated B-lymphocyte, its rapid cell division to produce a clone of plasma cells
and the resulting production of antibodies that react with the antigen is called clonal
selection. Sometimes several different antibodies react with the one antigen – this is
polyclonal selection.
7 After these antibodies have tackled the foreign matter and the disease threat is
overcome, the antibodies disappear from the blood and tissue fluid. So too do
the bulk of the specific B-lymphocytes and T-lymphocytes responsible for their
formation.
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antigen enters body (the required
trigger to initiate specific antibody
11
production)
B-lymphocytes T-lymphocytes
T-lymphocytes respond to antigens
macrophage on the surface of other cells
1 antigen binds to antibody
on B-lymphocyte cell surface membrane
MHC protein

3 macrophages engulf antigens by endocytosis,
MHC = major histocompatibility and then express this antigen on their MHC
complex proteins on the cell surface membrane
All cells have MHC protein unique to = antigen presentation
cells of the organism.
2 antigen taken up
by endocytosis and is
then expressed on
the cell surface membrane
at the MHC protein
T-lymphocyte
5 T-helper cell now binds to B-lymphocyte

with same antigen expressed – immediately activation
the B-lymphocyte is activated
= activated B-lymphocyte activation
4 T-lymphocyte binds (briefly) to macrophage that

presents an antigen and is activated –
it is now called an
6 activated B-lymphocyte T-helper cell
divides rapidly by mitosis,
forming a clone
of plasma cells
7 some activated B-lymphocytes and T-lymphocytes

T-helper cells survive in the body as memory cells,
and are able to initiate a more speedy response in
the event of reinfections
each plasma cell, packed with

RER, now mass-produces antibody
molecules and secretes them by
exocytosis
antibodies overcome antigen

e.g. by neutralising it, by causing
clumping together of cells to aid
engulfing by other macrophages,
or by precipitation of soluble antigens
▲ Figure 11.6 The stages in antibody production
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However, certain of these specifically activated B- and T-helper cells are retained in
the body as memory cells. These are long-lived cells, in contrast to plasma cells and
11 activated B-lymphocytes. Memory cells make possible an early and effective response
in the event of a re-infection of the body by the same antigen (Figure 11.7). This is the
basis of natural immunity.
Memory cells are primary response secondary response if same

retained in lymph nodes. to initial infection infection (antigen) returns
They allow a quick and
specific response if the response due to memory
same antigen reappears. plasma cells cells, i.e. person has
antibody concentration
11 Immunity
short-lived immunity
Figure 11.7 The profile

of antibody production
on infection and 5 days 5 days
reinfection time
Questions It is now helpful to summarise the complex roles of B- and T-lymphocytes in the
immune system (Figure 11.8).
2 Identify where
antigens and red bone marrow
– site of actively
antibodies may be dividing stem cells
found in the body.
3 Remind yourself of
the appearance of thymus
gland
the types of white
blood cells observed
in a blood smear blood circulation, tissue fluid,
preparation. See and lymph nodes
for example, the B-lymphocytes T-lymphocytes
photomicrograph
in Figure 8.6 in the presence of a specific antigen, memory cells
(page 172). Compare e.g. an invading pathogenic bacterium
this image with a
prepared slide of B-lymphocyte now antigen
a human blood carrying engulfed
antigen
smear so that you
are familiar with activated
the appearance of macrophage
phagocytic white
blood cells and
memory lymphocyte activated
lymphocytes. T-lymphocyte
Make a fully
annotated drawing activated T-lymphocyte
of representative becomes
activated T-helper cell
white blood cells
B-lymphocyte
that makes clear the
differences between
them. cell division to
form a clone of
plasma cells T-helper cell becomes
T-killer – destroys
cells infected by virus,
Figure 11.8 The roles of B- and or other cells carrying
T-lymphocytes in the immune antibody secreted, antigens e.g. TAA of
system – a summary antigen overcome cancer cells (see p234)
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11.2 Antibodies and vaccination
Learning outcomes 11
11.2.1 relate the molecular structure of antibodies to their functions
11.2.2 outline the hybridoma method for the production of monoclonal antibodies
11.2.3 outline the principles of using monoclonal antibodies in the diagnosis of
disease and in the treatment of disease
11.2.4 describe the differences between active immunity and passive immunity,

and between natural immunity and artificial immunity
11.2.5 explain that vaccines contain antigens that stimulate immune responses
to provide long-term immunity
11.2.6 explain how vaccination programmes can help to control the spread of
infectious diseases
Starting point
★ Active and passive immunisations are effective ways to treat and prevent
infectious diseases.
The antibody molecules – structure in relation to function

Antibodies are proteins called immunoglobulins. Each antibody consists of four
Agglutination polypeptide chains held together by disulfide bridges (–S–S–), forming a molecule in the
bacteria shape of a Y. The arrangement of amino acids in the polypeptides that form the tips of
the arms of the Ys in this molecule are unique to that antibody. It is these regions that
hold the highly specific binding site for the antigen. Antibodies initially occur attached
to the cell surface membrane of B-lymphocytes, but later are also mass-produced and
secreted by cells derived from the B-lymphocyte (Figure 11.10, overleaf), but only after
that B-lymphocyte has undergone an activation step.
Opsonisation The specific structure of the antibody enables it to carry out its function of binding with
bacterium a particular antigen and destroying it. These functions include:
» clumping (agglutinating) together pathogens, making it easier for macrophage
phagocyte
engulfment or to prevent the pathogens from reproducing or entering other cells
» tagging pathogens for later phagocytosis by macrophages (opsonisation)
» neutralising toxins by binding to them so they have no effect.
Neutralisation These functions are shown in Figure 11.9.
antibody
The structure of the antibody molecule (Figure 11.10, overleaf) demonstrates the four
levels of protein structure, discussed earlier (pages 49–50):
virus
The primary structure of a protein is the long chain of amino acids in its molecule – amino
acid residues joined by peptide bonds. You can see that there are four polypeptide chains
▲ Figure 11.9 Functions of
antibodies
that make up each antibody, two described as ‘heavy chains’ and two as ‘light chains’. The
polypeptides differ in the variety, number and order of their constituent amino acids.
The secondary structure of a protein develops when parts of the polypeptide chain
take up a particular shape, immediately after formation at the ribosome. Parts of the
chain become folded or twisted, or both, in various ways. The most common shapes
are formed either by coiling to produce an α-helix or folding into β-sheets, and both
shapes are permanent, held in place by hydrogen bonds.
The tertiary structure of a protein is the precise, compact structure, unique to that
protein that arises when the molecule is further folded and held in a particular complex
shape. This shape is made permanent by four different types of bonding, established
between adjacent parts of the chain (Figure 2.22, page 51).
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The quaternary structure of a protein arises when two or more proteins are bound together,
forming a complex, biologically active molecule. In an antibody, four polypeptide chains
11 are combined, held together in a characteristic shape by sulfide bridges (Figure 11.10).
Figure 11.10 The

antibody – a quaternary lymphoctyes are activated activated lymphocyte
protein when an antigen enters the divides rapidly producing
body and binds to a receptor a clone of identical cells
on the cell surface membrane
inactive
lymphocyte
11 Immunity
antigen
binding site variable region
of heavy chain
constant region
of heavy chain
variable region
of light chain
antibodies occur attached
constant
to the cell surface membrane l–S–S–l
region of
of B-lymphocytes disulfide
light chain
bridges
disulfide
bridge
cell surface
cytoplasm of membrane
B-lymphocyte
and may be secreted
by exocytosis as
free-standing molecules antibody-producing
lymphocyte
Figure 11.11 Computer-

generated image of an
antibody molecule
Monoclonal antibodies
We have seen that white blood cells in the blood provide our main defence against
the invasion of the body by harmful microorganisms. Special cells among the white
blood cells, called lymphocytes, are responsible for the immune response. Among
these it is the B-lymphocytes that secrete antibodies. Antibodies are very effective in
the destruction of antigens within the body (Figure 11.7). Monoclonal antibodies are
produced by a single clone of B-lymphocytes. They are identical antibodies effective
against a single, specific antigen.
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The production of monoclonal antibodies
Antibodies have great potential in modern medicine, if they can be made available.
The problem has been that B-lymphocytes are short-lived. This issue of the normally 11
brief existence of a B-lymphocyte is overcome by fusing the specific lymphocyte with
a cancer cell (a malignant myeloma of a B-lymphocyte) which, unlike non-cancerous
body cells, goes on dividing indefinitely. The fused cells, called hybridoma cells, are
separated and each hybridoma is cultured individually. Each cell divides to form a
clone of cells which persists and which conveniently goes on secreting the antibody in
significant quantities. The outcome is a single antibody that is stable and that can be

used over a period of time. How a specific monoclonal antibody is made is illustrated
in Figure 11.12.
The use of monoclonal antibodies in medicine is already established and is under
further development.
immune system of mouse

stimulated to produce
antibodies by injection of
an antigen
mouse spleen cells mouse tumour cells

cultured by tissue culture removed and cultured
spleen cells and tumour cells

are mixed and cultured
tumour cell hybridoma

some B-lymphocyte cells fuse
with tumour cells to produce
a hybrid cell called a hybridoma
B-lymphocyte
cells extracted, cultured separately, and the it is these hybridoma cells that
medium around each is tested for antibody must be detected, isolated and
(produced by hybridomas of B-lymphocytes cultured
fused with a tumour cell)
Question
4 Study the production
of monoclonal
antibodies illustrated
in Figure 11.12.
Make a concise list of
these cells, once isolated, are cultured
the sequence of steps and supply the monoclonal antibody
in their production.
▲ Figure 11.12 The formation of monoclonal antibodies
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The use of monoclonal antibodies in the treatment of disease
11 It is known that cancer cells carry specific tumour-associated antigens (TAA) on

their cell surface membrane. Monoclonal antibodies to TAA have been produced. Then,
drugs to kills cells or inhibitors to block key tumour proteins have been attached. The
monoclonal antibodies specifically target and kill the cancer cells. The advantage is that
whereas many drugs and treatments effective against cancer are also harmful to other,
healthy cells, the specificity of antibodies avoids this problem. These developments are
sometimes referred to as ‘magic bullets’.
Monoclonal antibodies have already been developed to treat certain cancers, as
11 Immunity
described in Table 11.1. Now, monoclonal antibodies are under investigation in clinical
trials for nearly every type of cancer. Perhaps this is the most important way that
monoclonal antibodies are currently being used in the treatment of disease.
Making cancer Cancer cells are ‘self’ cells – they have not invaded the body from outside. The immune system only
cells ‘visible’ targets non-self cells. Monoclonal antibodies that recognise and attach to cell surface membrane
to the immune proteins that have resulted from the specific cancer condition present have been produced. Once
system introduced into the body they attach, making the cell visible to the immune system and therefore
vulnerable to destruction by it.
Blocking growth Monoclonal antibodies have been produced that attach to and block the growth signal molecules on
signals of the the cell surface membrane of cancer cells. Unblocked, these growth factors signal the cancer cell to
cell surface grow. Cancer cells produce additional growth factors, enhancing their growth rate. Such ‘blocking’
membrane of monoclonal antibodies have been produced to treat colon cancer, for example.
cancer cells
Stopping the The growth signals manufactured by cancer cells which stimulate the growth of fresh blood vessels
formation of new to supply the developing malignant tumour can be blocked by specific monoclonal antibodies. One
blood vessels such is in use in the treatment of breast cancer.
Delivering Radiation sufficient to destroy a cancer cell can be delivered specifically to the cells of a malignant
radiation to tumour by combining radioactive particles with monoclonal antibodies that attach exclusively to
cancer cells cancer cells. These monoclonal antibodies deliver a low level of radiation over a long period of
time, without damage to the surrounding cells. Such monoclonal antibodies are in use against non-
Hodgkin’s lymphoma.
▲ Table 11.1 How monoclonal antibodies are used to treat cancers
Another application of monoclonal antibodies in the treatment of disease is as ‘passive

vaccines’. A monoclonal antibody specific to a particular pathogen may be produced and
injected into a patient’s blood circulation to good effect.
The use of monoclonal antibodies for pregnancy testing

Another application of monoclonal antibodies is in pregnancy testing. A pregnant
woman has a significant concentration of HCG hormone in her urine whereas a
non-pregnant woman has a negligible amount. Monoclonal antibodies to HCG have
been engineered which also have coloured granules attached. In a simple test kit,
the appearance of a coloured strip in one compartment provides immediate, visual
confirmation of pregnancy. How this works is illustrated in Figure 11.13.
Because all the monoclonal antibodies produced by a clone of a B-lymphocyte are
identical they can be used to identify other specific macromolecules, too.
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pregnancy testing kit
compartment with immobile antibodies to
11
the coloured granule–HCG monoclonal
antibody complex
compartment with immobile

HCG monoclonal antibodies
compartment with mobile HCG monoclonal

antibodies with blue coloured granules attached
wick dipped into

urine sample
a blue colour appears here
when the test has completed movement of urine
correctly by capillary action
a blue colour appears here if the
urine contains HCG (= pregnant)
how the positive test result is brought about
immobile antibodies to mobile HCG antibodies

coloured granule–HCG immobile HCG with blue coloured
antibody complex antibodies granules attached
HCG attaches to mobile HCG urine with HCG moving

antibodies with coloured granules up the test strip
these steps
take only a
few minutes
immobile antibodies trap the mobile

HCG antibodies with coloured granules,
so a blue colour appears in window
EXTENSION
An issue to note is
that, because the
original monoclonal
antibodies were excess mobile HCG antibodies with
coloured granules move on up the test
developed from mice strip and combine with the immobile
cells (Figure 11.12), a antibodies here, giving a second blue
patient may develop colour confirming the test is completed
(this colour appears whether or not
an adverse reaction there is HCG in the urine)
to an antibody. ▲ Figure 11.13 Detecting pregnancy using monoclonal antibodies
This is because the
monoclonal antibody
is itself a foreign Other examples of the use of monoclonal antibodies in diagnosis
protein to the patient’s » Since a B-lymphocyte recognises a specific antigen, monoclonal antibodies can be
immune system. used to distinguish between different strains of a disease-causing microorganism
Genetically engineered
» Detection of HIV in a patient’s blood sample
antibodies that are
» Blood typing before a blood transfusion, for example to determine A, B, AB or O and
compatible with
Rhesus negative or Rhesus positive groupings
the human immune
system are sought to » Tissue typing before a transplant operation
avoid the triggering of » Identification of the particular type of leukaemia (a cancer) that a patient has
the immune response. contracted to determine the most appropriate treatment
» Location of tumours.
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Types of immunity
11 Our immune system may provide protection to the body from the worst effects of many
of the pathogens that may invade. This immunity may be acquired actively, as when our
body responds to invasion by a pathogen, or passively, as when ready-made antibodies
are injected into our body. Also, immunity may be acquired naturally, as when our
bodies respond to a natural pathogen invasion, or artificially, as follows vaccination
(artificial immunity).
In Table 11.2 the differences between active and passive immunity, and natural and
11 Immunity
artificial immunity are identified and illustrated.
Questions . . . and their

Types of immunity Natural Artificial longevity
5 a Identify the steps
to plasma cell Active immunity e.g. Immunity that e.g. Immunity Active immunity
formation that » Results from exposure follows natural that results from persists for
the existence of to an antigen. During infection by a the injection of a prolonged
memory cells the subsequent immune pathogen involving antigens (such as period, and
avoids in the event response, antibodies the production of those attached to possibly
of re-infection. are produced by plasma memory cells (for killed or weakened throughout life,
cells. example, natural pathogens) where after it has been
b Why is it quicker infection with memory cells are acquired because
to respond on » There is a delay before chicken pox, giving made (for example, the body makes
re-infection in the immune response
long-term protection after vaccination). memory cells.
these cases? is complete. (Immunity
from this virus).
6 State what we mean takes some days to
by immunity. build up.)
Passive immunity e.g. Immunity e.g. Immunity Passive immunity
» Involves the transfer following transfer of following injection fades with time
of antibodies (already maternal antibodies of antibodies because the
made in the body of into a fetus through (for example, recipient does
another organism or the placenta, and monoclonal not acquire
in vitro) into the body into a newborn antibodies, memory cells
where they will bind to infant in the first to treat acute and so is unable
their specific antigen milk (colostrum). life-threatening to make the
if it is present. infections, such as antibodies in
rabies). future.
» Gives instant
immunity.
▲ Table 11.2 Types of immunity that humans display
Vaccination
Vaccination is the deliberate administration of antigens that have been made harmless,
after they are obtained from disease-causing organisms, in order to confer long-term
immunity in future. The practice of vaccination has made important contributions to
public health (see the example of tuberculosis that starts on page 208).
Vaccines are administered either by injection or by mouth. They cause the body’s
immune system to briefly make antibodies against the disease (without becoming
infected), and then to retain the appropriate memory cells. Active artificial immunity
is established in this way (Table 11.2). The profile of the body’s response in terms of
antibody production, if later it is exposed to the antigen again, is exactly the same as if
the immunity was acquired after the body overcame an earlier infection.
Vaccines are manufactured from dead or attenuated (weakened) bacteria, or from
inactivated viruses, or purified polysaccharides from bacterial walls, or toxoids, or even
recombinant DNA produced by genetic engineering.
In communities and countries where vaccines are widely available and have been
taken up by 85–90 per cent of the relevant population, vaccination has reduced some
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previously common and dangerous diseases to very uncommon occurrences. As a result,
in these places, the public there has sometimes become casual about the threat such
diseases still represent. 11
Question Success of vaccination programmes
7 a By means of a Vaccination has been so successful that some formerly common and dangerous diseases
table such as have become very uncommon occurrences in many human communities. For example,
Table 11.2, show vaccination has led to the worldwide eradication of smallpox and to a great reduction in
the ways that the incidence of measles, polio and tetanus.

immunity may
arise according Herd immunity
to whether it Interestingly, it is not essential for everyone in a population to be immunised against a
is actively or contagious disease in order to control that disease. The herd immunity theory proposes
passively obtained, that the risk of someone who is susceptible to a contagious disease becoming infected
and by natural or reduces, the greater the proportion of people in that community who are immune. To
artificial means. take an extreme example, if all but one person in the UK is immune to a contagious
Place these terms disease, the chance of the one susceptible person being exposed to the pathogen within
in your table: the UK is almost nil.
polio vaccine
You might be wondering what proportion of a population could avoid vaccination but
measles infection still be protected by the majority who have been vaccinated. This depends on the nature
antibodies received of the disease-causing organism and its method of transmission. Table 11.3 provides
via the placenta information about a number of contagious diseases with which you might be familiar.
monoclonal
antibodies to treat Percentage threshold to
tetanus Disease Transmission route achieve herd immunity
b Underline those Diphtheria Via saliva 85%
terms in which Measles Airborne 83–95%
memory cells
Mumps Droplet 75–86%
are not formed
(and therefore the Rubella Droplet 83–85%
effects are short ▲ Table 11.3 The threshold percentage of the population needed to achieve herd immunity
term).
Looking at Table 11.3, you might think it will be safe for you to avoid immunisation.
Remember, though, you are dealing with a mathematical model concerned with
reducing the likelihood of infection. The likelihood of being knocked down by an
automobile is low, but you still look both ways before crossing a road. It is best to
restrict failure to immunise or vaccinate to those who might be harmed by it, such as
people with weakened, or compromised, immune systems.
Given the success of vaccination programmes in eradicating contagious diseases, the
public has sometimes become casual about the threat such diseases still pose.
During your GCSE science course, you probably studied the effects of a newspaper
article suggesting a link between a vaccine to protect against measles, mumps and
rubella (the combined MMR vaccine) and autism. As a result of this article, so many
parents declined the invitation to have their children vaccinated that the proportion of
vaccinated children fell below the herd immunity threshold in some communities. The
doctor who proposed this link to autism was subsequently discredited.
The World Health Organization (WHO) had declared the UK free of measles in 2016
but it lost this status three years later. There were 991 confirmed cases in England and
Wales in 2018. The majority of these cases were among older teenagers and people in
their early 20s who did not receive the MMR vaccination when they were younger.
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SUMMARY
11 » Defence against disease that enters when the production and the retention of appropriate
body is wounded and then invaded by a pathogen memory cells.
is provided by phagocytic white blood cells. These » Monoclonal antibodies are a source of a
are able to engulf and destroy foreign matter. single antibody made by a particular type of
» The immune system is provided by B- and B-lymphocyte fused with a cancer cell to form
T-lymphocytes which, when sensitised by foreign a hybridoma. This divides indefinitely and so
material (antigens), respond in complex ways to secretes the antibody in significant quantities.
11 Immunity
overcome the invasion, including by the production Monoclonal antibodies are used in the treatment of
of specific antibodies that destroy or inactivate cancer by targeting specific damaged or diseased
the foreign matter. Memory cells are formed and cells and killing them by the delivery of a ‘magic
retain the ability to respond again in the event of bullet’. They are used in diagnosis to identify
reinfection. the presence of specific macromolecules, as in
» Vaccination is the deliberate administration of pregnancy testing, and in several other medical
antigens that have been rendered harmless applications.
but nevertheless are able to stimulate antibody

1 Fig. 1.1 is a diagram that shows the structure of an antibody molecule.
variable variable
region region
constant
region
▲ Fig. 1.1
a State why the antibody molecule shown in Fig. 1.1 has quaternary structure. [1]
b i Use Fig. 1.1 to explain how the structure of the variable region of an antibody
molecule is related to its function. [3]
ii State the role of the constant region of an antibody. [1]
c Monoclonal antibodies are used both in diagnosis and in treatment of disease.
i Outline how monoclonal antibodies are produced. [4]
ii Suggest the advantages of using monoclonal antibodies in diagnosis of
disease. [2]
[Total: 11]
2 a P
lasma cells secrete specific antibodies but are short-lived in the body.
Explain, with use of a diagram, how a plasma cell is made ‘immortal’ in the
production of a monoclonal antibody. [8]
b Detail the use of monoclonal antibodies in one application of their use in
diagnosis and one application in the treatment of diseases. [8]
[Total: 16]
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3 Phagocytes and lymphocytes are part of the body’s cellular response to infection
by pathogens.
Fig. 3.1 shows the origin and maturation of phagocytes and lymphocytes. 11

D
mature
cells
C
A B Not to scale
▲ Fig. 3.1
a Name the site of origin of phagocytes and lymphocytes. [1]
b Name
i cells A, B and C [3]
ii organ D. [1]
c Explain the roles of the cells A, B and C in an immune response.
In your answer use the terms antigen and non-self. [5]
[Total: 10]
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A LEVEL

Energy is a fundamental Learning outcomes

concept in biology. All living
things require a source of
cellular energy to drive 12.1.1 outline the need for energy in living organisms, as illustrated by active
their various activities. transport, movement and anabolic reactions, such as those occurring in
All organisms respire by DNA replication and protein synthesis
using enzyme-catalysed 12.1.2 describe the features of ATP that make it suitable as the universal energy
reactions to release energy currency
from energy-rich molecules
12.1.3 state that ATP is synthesised by: transfer of phosphate in substrate-
such as glucose and fatty
acids and transfer that
linked reactions, and chemiosmosis in membranes of mitochondria and
energy to ATP. ATP is the chloroplasts
universal energy currency 12.1.4 explain the relative energy values of carbohydrates, lipids and proteins as
in cells. In eukaryotes, respiratory substrates
aerobic respiration occurs in 12.1.5 state that the respiratory quotient (RQ) is the ratio of the number of
mitochondria. molecules of carbon dioxide produced to the number of molecules of
The practical activities in oxygen taken in, as a result of respiration
this topic give opportunities 12.1.6 calculate RQ values of different respiratory substrates from equations for
for candidates to plan respiration
investigations, analyse and 12.1.7 describe and carry out investigations, using simple respirometers, to
interpret data and evaluate
determine the RQ of germinating seeds or small invertebrates (e.g.
experimental procedures
and the quality of the data
blowfly larvae)
collected.
Starting point
★ ATP is the universal energy currency as it provides the immediate source of
energy for cellular processes.
12.1 Energy
Cell respiration – the controlled transfer of energy
Living things need a continuous transfer of energy to keep them alive and active.
Energy is used to build, maintain and repair body structures, and for all the activities
of life. Energy is transferred in cells by the breakdown of nutrients. Typically, it is
carbohydrates like glucose from which energy is transferred by the process of cellular
respiration. It is respiration that is the subject of this topic.
So organisms need a supply of certain nutrients for respiration, but animals and plants
obtain these in very different ways.
Green plants make sugars from simpler substances by photosynthesis. In photosynthesis
they transfer light energy into the chemical potential energy of sugars. Using these
sugars and a supply of ions from the soil, they make their proteins, lipids and all other
requirements. This type of nutrition is called autotrophic. It means ‘self-feeding’.
Photosynthesis is discussed in Topic 13.
On the other hand, animals and other heterotrophic organism are dependent on green
plants for their nutrients – directly or indirectly. Their nutrients are taken up into their
body tissues following the digestion of food.
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glucose burning in air sprinters completing a race
12
12.1 Energy
energy change in burning energy change in cellular respiration
glucose glucose + oxygen

+ oxygen
energy in molecules
energy in molecules energy transferred

to ATP in many
energy lost as small steps (ATP
heat then used
in muscular
contraction)
CO2 + H2O
CO2 + H2O
time time
▲ Figure 12.1 Combustion and respiration compared
People sometimes talk about ‘burning up food’ in respiration. In fact, linking respiration
to burning (combustion) is unhelpful. In combustion, energy in fuels is released, in a
one-step reaction, as heat. Such a violent change would be a disaster for body tissues.
In cell respiration, a large number of small steps occur. Each is catalysed by a particular
enzyme. Because energy in respiration is transferred in small quantities, much of the
energy is made available to the cells. It may be trapped in the energy currency molecule
adenosine triphosphate (ATP). However, some energy is still lost as heat in each step
(Figure 12.1). In animals that regulate their body temperature, this source of heat is
important.
The need for energy in living organisms

Energy is needed for all the activities of living organisms, such as nutrition, excretion,
sensitivity, movement and reproduction. It is also required to build and maintain body
structures, and to maintain body temperature. Specifically, all organisms transfer usable
energy for:
» the reactions of metabolism, and especially for the steps by which complex
molecules are built up, including macromolecules. All these reactions are known as
anabolism. Protein synthesis is just one example.
» the active transport of molecules and ions across membranes, carried out by
membrane pumps.
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» movement by organisms, including those due to muscle contractions. Energy is also
transferred for movements within cells and by cell organelles.
12 » formation and secretion of substances from cells, including enzymes and hormones.
» cell division and DNA replication, and the formation and maintenance of all the
organelles of the cytoplasm.
ATP – the universal energy currency

Adenosine triphosphate (ATP) is a relatively small, soluble organic molecule. It occurs
in all cells, typically at a concentration of 0.5–2.5 mg cm–3. Like many organic molecules
of its size, it contains a good deal of chemical energy locked up in its structure.
Chemically, ATP is a nucleotide (page 121), but it has a particular structural feature we have
not seen in nucleotides previously – it has three terminal phosphate groups linked together
in a linear sequence (Figure 12.2). These phosphate groups are involved in ATP’s role in cells.
NH2
N O O–
N
O P O
N O CH2 P O O P O–
N
O
–O O–
phosphate
H H
OH OH
adenine phosphate phosphate
ribose
adenosine triphosphate ATP

adenosine diphosphate ADP
Figure 12.2 ATP, ADP adenosine monophosphate AMP
and AMP
ATP is referred to as energy currency because, like money, it can be used in different
Question
contexts and it is constantly recycled in the living cell. When the outermost phosphate
1 In Figure 12.2 the is removed, adenosine diphosphate (ADP) is formed and energy is transferred.
structural formula
Later, it is energy transferred from respiration that reforms ATP from ADP and
of ATP is shown.
phosphate (Pi). The reactions that yield energy and generate ATP from ADP and
In Figure 6.1
(page 121) the way phosphate (Pi) are particular steps in respiration. We will return to these shortly.
the components All these changes make up the ATP–ADP cycle (Figure 12.3).
of nucleotides
are represented ATP is formed during sugar + oxygen carbon dioxide
diagrammatically respiration. + water
is shown. Use
the symbols in
Figure 6.1 ADP + Pi ATP
to represent the
structure of ATP.
+H2O
metabolic reactions and metabolic processes

driven by energy transferred from ATP, e.g.
• movement of materials across cell membranes
• building molecules, including macromolecules
and other biomolecules
Figure 12.3 The ATP– • movements by muscle contraction, and other
ADP cycle cell movements
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The free energy available in the step from ATP to ADP is approximately 30–34 kJ mol–1.
Some of this energy is lost as heat in the reaction, but much of the free energy is made
available to do useful work – more than sufficient to drive a typical energy-requiring
reaction of metabolism, for example. Actually, ATP may lose both of the outer phosphate
12
groups, but normally only one is lost. It is only in a few reactions that more energy is
required and in these cases both may be lost.
An important way in which ATP serves as a reservoir of usable chemical energy is its role as
a common intermediate between energy-yielding reactions and energy-requiring reactions
and processes. We saw an example of this in protein synthesis (Figure 6.14, page 134). There
12.1 Energy
are other ways in which energy is transferred, including muscle contraction (page 255).
In summary, ATP is a molecule universal to all living things. It is the source of energy for
chemical change in cells, tissues and organisms. The important features of ATP are that it is:
» a substance that moves easily within cells and organisms – by facilitated diffusion
» formed in cellular respiration and takes part in many reactions of metabolism
» able to transfer energy in relatively small amounts, sufficient to drive individual reactions.
In the course of the ATP–ADP cycle in cells:
» ATP is formed from adenosine diphosphate (ADP) and phosphate ions (Pi) by the
Question
transfer of energy in respiration
2 Outline why ATP is » in the presence of specific enzymes, ATP is involved in energy-requiring reactions.
an efficient energy
We will return to the issue of just how the energy of ATP brings about useful work in
currency molecule.
cells and organisms shortly. We will focus on the process of cellular respiration first.
EXTENSION
Respiration as a series of redox reactions oxidation and reduction reactions. The shorthand name
for reduction–oxidation reactions is redox reactions.
The terms ‘oxidation’ and ‘reduction’ occur frequently
in respiration. First, we need to remind ourselves what Redox reactions take place in biological systems
is meant by these terms. because of the presence of a compound with a strong
tendency to take electrons from another compound
In biological oxidation, oxygen atoms may be added (an oxidising agent) or the presence of a compound
to a compound. Alternatively, hydrogen atoms may with a strong tendency to donate electrons to another
be removed. In respiration, all the hydrogen atoms compound (a reducing agent).
are gradually removed from glucose. They are added
to hydrogen acceptors, which are then reduced. In Another feature of oxidation and reduction is an energy
respiration, most of the hydrogen atoms are added to the change. When reduction occurs, energy is absorbed (it
hydrogen acceptor molecule known as nicotinamide is an endergonic reaction). When oxidation occurs,
adenine dinucleotide (NAD). The process of energy is released (an exergonic reaction). An example
removal of hydrogen from a compound is known as of energy release during oxidation is the burning of a
dehydrogenation and the enzyme involved in such a fuel in air. Here, energy is given out as heat. In fact, the
reaction is called a dehydrogenase. amount of energy in a molecule depends on its degree
of oxidation. An oxidised substance has less stored
Now a hydrogen atom consists of an electron and a energy than a reduced substance. An example of this is
proton. This means that in a reduction reaction, one or the fuel molecule methane (CH4) which has more stored
more electrons are gained. In fact, the best definition of chemical energy than carbon dioxide (CO2).
oxidation is the loss of electrons and of reduction is
the gain of electrons. So tissue respiration is a series of
The role of nucleotides in cell biochemistry

In addition to being the building blocks of the nucleic acids, certain nucleotides and
molecules made from nucleotides are important in the metabolism of cells. An example
is adenosine triphosphate (ATP). The structure and roles of ATP were introduced in
Topic 1 (page 22). In Figure 12.2 we viewed the structure of ATP as a nucleotide.
Look at the details of the structure and roles of ATP in these references again, now.
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Other nucleotides involved in respiration
12 1 Nicotinamide adenine dinucleotide (NAD)

NAD consists of two nucleotides combined with two phosphate groups (Figure 12.4).
In one of the combined nucleotides, the organic base is replaced by a substance
called nicotinamide. Nicotinamide is derived from a vitamin of the B complex, called
nicotinic acid. The importance of the ring molecule, nicotinamide, is that it accepts
hydrogen ions and electrons. When NAD accepts electrons it is said to be reduced,
but it can pass them to other acceptor molecules with relative ease. When reduced
NAD passes electrons on, it has become oxidised again. The transport of hydrogen
ions like this is an important aspect of respiration. NAD is a substance known as a

coenzyme, which works with different enzymes of respiration. It also takes part in
other processes in cells.
2 Flavine adenine dinucleotide (FAD)
FAD is a coenzyme derived from vitamin B2. Like NAD this is a hydrogen-carrying
molecule involved in oxidation and reduction reactions, including in the Krebs cycle
(Figure 12.9, page 251). It occurs tightly associated with protein, forming a complex
known as a flavoprotein.
Figure 12.4 NAD, NAD is a ‘carrier’ of hydrogen ions

structure and role and electrons in respiration H
CONH2
adenine nicotinamide
+
N
O O
ribose Pi Pi ribose action end (hydrogen
ion transport)
‘rest of molecule’, recognised by enzymes

with which NAD is a coenzyme
mode of action:
summary:
NAD + + 2H + + 2e– NADH + H +
changes at ‘action end’:

H H H
CONH2 + 2H + + 2e– CONH2 + H +
+
N N
in these states the molecule is referred to as:

oxidised NAD reduced NAD
3 Coenzyme A (CoA)
CoA is involved in the removal of two-carbon fragments from certain carbohydrates
and lipids during respiration, and also in food-storage reactions. You can see CoA ‘at
work’ in the link reaction of cell respiration (Figure 12.9, page 251).
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flavine adenine dinucleotide (FAD) coenzyme A (CoA)
12
flavine
phosphate pantothenic
adenine adenine groups acid (a vitamin)
O
Pi Pi ribose Pi Pi S C CH3
sugar pentose two-carbon fragment

alcohol (acetyl unit) in transport
12.1 Energy
▲ Figure 12.5 Other nucleotide derivatives involved in respiration
The ways ATP is generated in respiration – an introduction

We have seen that ATP is synthesised in cells from ADP and inorganic phosphate. This
occurs in respiration in two ways.
1 Transfer of phosphate in substrate-linked reactions takes place within the cytosol
of cells forming part of the cell respiration pathway called glycolysis. The steps to
glycolysis are listed in order, on page 250, and the reactions by which substrate-level
phosphorylation is brought about (Step 3. Oxidation, and Step 4. ATP synthesis) are
shown in Figure 12.8.
Look up these references now.
Actually, the reactions of substrate-level phosphorylation occur twice in glycolysis,
and it also occurs in the Krebs cycle. However, the amount of ATP generated by this
mechanism is trivial.
2 Chemiosmosis in membranes of mitochondria and chloroplasts (Figure 12.11,
page 254). The bulk of ATP synthesis takes place in special structures associated
with the electron transport chain, present in the membrane-bound organelles, the
mitochondria (page 17) and also in green plants in the chloroplasts (page 19),
as we shall shortly discuss (see ‘The electron transport chain and oxidative
phosphorylation’, pages 252–3).
EXTENSION
The respiration of fats and proteins vigorous physical exercise can help in body weight
reduction.
In addition to glucose, fats (lipids) are also commonly
used as respiratory substrates – first being broken Proteins are also used as respiratory substrates by
down to fatty acids and glycerol, page 45. animals, especially carnivorous animals. Proteins are
first hydrolysed to amino acids. Then, individual amino
Fatty acids are ‘cut up’, by enzyme action of course, into acids are deaminated. (That is, the amino group, –NH2,
2-carbon fragments. These are then fed into the Krebs is split off and excreted, as ammonia or urea, for
cycle via coenzyme A. Vertebrate muscle (including our example.) The residual carbon compound, an organic
heart muscle) is well adapted to the respiration of fatty acid, then enters the respiratory pathway as pyruvic
acids in this way and they are just as likely as glucose acid and acetyl coenzyme A, or as a Krebs cycle acid.
to be the respiratory substrate. This is one reason why
The relative energy values of carbohydrates, lipids

and proteins as respiratory substrates
The energy value of respiratory substrates is expressed in joules (J) and kilojoules
(kJ, 1 kJ = 1000 J). We have seen that this may be estimated experimentally, using a
calorimeter (Figure 12.6). The typical amounts of energy that the major food substances
yield are as follows:
carbohydrates: 1600–1760 kJ per 100 g
lipids (fats and oils): 3700–4000 kJ per 100 g
protein: 1700–1720 kJ per 100 g
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Why do lipids (and proteins) transfer more energy than carbohydrates?
12 The greater part of the energy transferred in aerobic respiration comes from
the oxidation of reduced NAD and the formation of water (during oxidative
phosphorylation). So, the greater the amount of hydrogen in a particular respiratory
Question substrate, the greater is its energy value.
3 Explain why the Triglycerides are the form in which lipids are respired. Triglycerides contain more
amino group must hydrogen in each molecule than carbohydrates. Mass for mass, fats and oils release more
be removed from than twice as much energy when they are respired as carbohydrates do. In effect, fats
amino acids and be are more reduced than carbohydrates – they therefore form a more concentrated energy
converted to urea store than carbohydrates.

before the remainder Although the primary purpose of the protein in food is to provide the amino acids
of the molecule can for the production and maintenance of the body’s proteins, we must remember that
be safely respired. they may also be broken down to provide energy. In other words, a secondary role
of proteins, when present in excess, is as a supplementary energy source. However,
proteins must first be deaminated before respiration can occur safely. And you can see
from the energy values given on the previous page that the carbon in proteins is slightly
more reduced than that in carbohydrates.
EXTENSION
Measuring the energy of nutrients
Samples are
We can estimate the total energy in a common
stirrer (ensures thermometer nutrient such as glucose by means of a simple
completely even distribution
oxidised in of heat)
calorimeter (Figure 12.6). Here, a known
air. mass of glucose is placed in the crucible in a
closed environment. It is then burnt in oxygen.
The energy available is released as heat and is
heat-transfer insulation transferred to the surrounding jacket of water.
coil The resulting rise in temperature of the water
is measured. This enables us to calculate the
energy value of the glucose sample. This is
because it takes 4.2 joules ( J) of heat energy to
The energy values of
foods are published food sample crucible with raise 1 g of water by 1°C.
in tables, and those is ignited here weighed
of manufactured sample One well known outcome of this technique is
and packaged foods the energy values of manufactured foods that
may be recorded on we may read on the packaging. In countries
the wrapping. oxygen
inlet where food is plentiful there is often much talk
about so-called ‘low-calorie’ items – the basis
▲ Figure 12.6 A calorimeter for measuring energy values
of ‘slimming’ diets.
Respiratory quotient
The respiratory quotient (RQ) is the ratio of the number of molecules of carbon
dioxide produced to the number of molecules of oxygen taken in, as a result of
respiration.
CO2 produced
RQ 5
O2 taken in
e.g. for a carbohydrate:
C6H12O6 1 6O2 S 6CO2 1 6H2O
6
RQ 5 51
6
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e.g. for a lipid:
2C57H110O6 1 163O2 S 114CO2 1 110H2O
12
114
RQ 5 5 0.7
163
Calculation of the respiratory quotient is useful because it may indicate which substrates
are being used. For example, when hexose sugars are respired aerobically:
C6H12O6 1 6O2 S 6CO2 1 6H2O
12.1 Energy
the respiratory quotient is:
CO2 produced
RQ 5
O2 taken in
6
5 51
6
Whereas, when fatty acids are respired aerobically:
C18H36O2 1 26O2 S 18CO2 1 18H2O
the respiratory quotient is:
CO2 produced
RQ 5
O2 taken in
18
5 5 0.7
26
The respiratory quotient due to the respiration of fat (RQ 5 0.7) is significantly lower
than when carbohydrates are respired (RQ 5 1.0). This is because fats have a greater
proportion of hydrogen relative to oxygen (they are a more highly reduced form of
respiratory substrate than sugars). More oxygen is required for the respiration of fats.
The respiratory quotient when proteins and amino acids are respired is typically
0.9. Where proteins are used as the substrate, we have noted that the amino group
(–NH 2) has first to be removed (deamination). In mammals the amino group
is converted to urea and excreted. Plants rarely respire proteins. If they did, the
ammonia gas formed would be harmful if not quickly lost from the cells of the
organism.
Despite this clear difference in values for different respiratory substrates, respiratory
quotient studies have only limited value. Rarely will an organism (such as germinating
seeds) be respiring a single respiratory substrate. Many organisms are found to have a
respiratory quotient of 0.8–0.9, but this may be due to respiration of both hexose sugars
(such as glucose) and fatty acids, in varying proportions.
Questions 4 Calculate the respiratory quotient of the saturated fatty acid, palmitic acid
(C15H31COOH).
5 The respiratory quotient (RQ) of two species of germinating seeds was measured at
two-day intervals after germination.
Day 2 4 6 8 10
Seedling A 0.65 0.35 0.48 0.68 0.70
Seedling B 0.70 0.91 0.98 1.0 1.0
a Plot a graph to compare the changes in respiratory quotient of the two species
during early germination.
b Suggest which respiratory substrates may be being respired.
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12.2 Respiration
12.2.1 state where each of the four stages in aerobic respiration occurs
in eukaryotic cells: glycolysis in the cytoplasm, link reaction in the
mitochondrial matrix, Krebs cycle in the mitochondrial matrix, oxidative
phosphorylation on the inner membrane of mitochondria
12.2.2 outline glycolysis as phosphorylation of glucose and the subsequent
splitting of fructose 1,6-bisphosphate (6C) into two triose phosphate

molecules (3C), which are then further oxidised to pyruvate (3C), with the
production of ATP and reduced NAD
12.2.3 explain that, when oxygen is available, pyruvate enters mitochondria to
take part in the link reaction
12.2.4 describe the link reaction, including the role of coenzyme A in the transfer
of acetyl (2C) groups
12.2.5 outline the Krebs cycle, explaining that oxaloacetate (4C) acts as an
acceptor of the 2C fragment from acetyl coenzyme A to form citrate (6C),
which is converted back to oxaloacetate in a series of small steps
12.2.6 explain that reactions in the Krebs cycle involve decarboxylation and
dehydrogenation and the reduction of the coenzymes NAD and FAD
12.2.7 describe the role of NAD and FAD in transferring hydrogen to carriers in
the inner mitochondrial membrane
12.2.8 explain that during oxidative phosphorylation: hydrogen atoms split into
protons and energetic electrons; energetic electrons release energy as
they pass through the electron transport chain (details of carriers are
not expected); the released energy is used to transfer protons across
the inner mitochondrial membrane; protons return to the mitochondrial
matrix by facilitated diffusion through ATP synthase, providing energy for
ATP synthesis (details of ATP synthase are not expected); oxygen acts as
the final electron acceptor to form water
12.2.9 describe the relationship between the structure and function of
mitochondria using diagrams and electron micrographs
12.2.10 outline respiration in anaerobic conditions in mammals (lactate
fermentation) and in yeast cells (ethanol fermentation)
12.2.11 explain why the energy yield from respiration in aerobic conditions
is much greater than the energy yield from respiration in anaerobic
conditions (a detailed account of the total yield of ATP from the aerobic
respiration of glucose is not expected)
12.2.12 explain how rice is adapted to grow with its roots submerged in water,
limited to the development of aerenchyma in roots, ethanol fermentation
in roots and faster growth of stems
12.2.13 describe and carry out investigations using redox indicators, including
DCPIP and methylene blue, to determine the effects of temperature and
substrate concentration on the rate of respiration of yeast
12.2.14 describe and carry out investigations using simple respirometers to
determine the effect of temperature on the rate of respiration
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Starting points
★ Respiration is the process whereby energy from complex organic molecules
is transferred to ATP.
12
★ This process of ATP synthesis using the energy in proton gradients is common
to both respiration and photosynthesis.
★ Some organisms and some tissues are able to respire in both aerobic and
anaerobic conditions. When yeast and plants respire under anaerobic
conditions, they produce ethanol and carbon dioxide as end-products;
mammalian muscle tissue produces lactate when oxygen is in short supply.
12.2 Respiration
Aerobic respiration
Cellular respiration which requires oxygen from the air is called aerobic respiration.
Most animals and plants and very many microorganisms respire aerobically. They do so
most, if not all the time.
In aerobic respiration, sugar is oxidised to carbon dioxide and water and much energy is
transferred. The steps of aerobic respiration are summarised by a single equation. This
equation is equivalent to a balance sheet of inputs (the raw materials) and outputs (the
products). It tells us nothing about the steps.
glucose 1 oxygen S carbon dioxide 1 water 1 energy
C6H12O6 1 6O2 S 6CO2 1 6H2O 1 2870 kJ
So, the most significant outcome of aerobic respiration is the large quantity of energy
that is transferred to ATP when glucose is oxidised. To understand how this energy is
transferred from glucose, we need to look into the steps of aerobic respiration.
The stages of aerobic respiration

In cellular respiration, glucose undergoes a series of enzyme-catalysed oxidation reactions.
These reactions are grouped into three major stages and a link reaction (Figure 12.7):
» glycolysis, in which glucose is converted to pyruvate
» a link reaction, in which pyruvate is converted to acetyl coenzyme A (acetyl CoA)
» the Krebs cycle, in which acetyl coenzyme A is converted to carbon dioxide
» the electron transport chain and oxidative phosphorylation, in which hydrogen
atoms removed in the oxidation reactions of glycolysis, the link reaction and the
Krebs cycle are converted to water. Most of the ATP is synthesised in this stage
(oxidative phosphorylation).
glucose oxygen
stages in tissue link

respiration reaction
ADP ADP
+ Pi + Pi
H
glycolysis Krebs
cycle hydrogen
atoms
electron
transport
chain
products some ATP carbon dioxide water much ATP
some ATP
Figure 12.7 The stages of aerobic respiration

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Glycolysis
12 Glycolysis is a linear series of reactions in which 6-carbon sugar is broken down to two
molecules of the 3-carbon pyruvate ion (Figure 12.8). The enzymes of glycolysis are located
in the cytoplasm outside organelles (known as the cytosol) rather than in the mitochondria.
Glycolysis occurs in four steps.
» Phosphorylation by reactions with ATP. In this way glucose is first activated. The
product is a six-carbon sugar with two phosphate groups attached – fructose 1,6
bisphosphate. Note that, at this stage of glycolysis, rather than producing ATP, two
molecules of ATP are consumed per molecule of glucose respired.
» Lysis (splitting) of fructose 1,6 bisphosphate now takes place, forming two molecules
of a three-carbon sugar called triose phosphate.
» Oxidation of the triose phosphate molecules occurs by removal of hydrogen, catalysed
by a dehydrogenase enzyme. The enzyme for this reaction (a dehydrogenase) works
with a coenzyme, nicotinamide adenine dinucleotide (NAD). NAD is a molecule
that can accept hydrogen. It then becomes reduced NAD. (Later, reduced NAD will
pass hydrogen ions and electrons on to other acceptor molecules. When it does, it is
oxidised back to NAD.)
» ATP synthesis. This happens twice in the reactions by which each triose
phosphate molecule is converted to pyruvate. This form of ATP synthesis is known
as at substrate level. It is quite different from the way the bulk of ATP synthesis
occurs later in cell respiration (during the operation of the electron transport
chain, see page 252).
Changes to the carbon skeleton in glycolysis

glucose
C C C C C C
2 × ATP glucose
1 Phosphorylation
ATP
(uses ATP) glucose is a relatively unreactive molecule
ADP
– reaction with ATP activates glucose
P
fructose 1,6 bisphosphate C C C C C C

(a 6-carbon sugar)
ATP
2 Lysis ADP
(splitting of the fructose 1,6 bisphosphate (6-carbon sugar) is split
into two triose phosphate (3-carbon sugar phosphates) P P
6-carbon backbone)
C C C C C C
2 × triose phosphate
(2 × 3-carbon sugar phosphate) +
P inorganic P
Pi phosphate P
3 Oxidation 2 × NAD+ P P P
+ addition of Pi
C C C C C C
inorganic phosphate 2 × reduced NAD ADP ADP
ATP ATP
4 × ADP
P P
4 ATP synthesis
at the substrate level 4 × ATP C C C C C C
ADP ADP
For each molecule of glucose: triose phosphate molecules
2 molecules of ATP are used are converted to pyruvate ATP ATP
4 molecules of ATP are formed.
2 × pyruvate C C C C C C
There is a net gain of 2
pyruvate pyruvate
molecules of ATP.
▲ Figure 12.8 Glycolysis: a summary
So, at this stage, as two molecules of triose phosphate are converted to pyruvate, four
molecules of ATP are synthesised. In total, there is a net gain of two molecules of ATP
during glycolysis.
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The link reaction and the Krebs cycle
The subsequent stages of aerobic respiration occur in the organelles known as
mitochondria. 12
Remind yourself of the size and structure of the mitochondrion now (Figure 1.16,
page 17). Notice the tiny gap between the inner and outer membranes.
Question When oxygen is available for aerobic respiration, pyruvate is actively transported from
the cytosol into the matrix of a mitochondrion to take part in the link reaction. There
6 State which of it is metabolised. Firstly, carbon dioxide is removed from the 3-carbon pyruvate, a
the following are
12.2 Respiration
reaction called decarboxylation. At the same time, oxidation occurs by removal of
produced during hydrogen, catalysed by a dehydrogenase enzyme. NAD is converted to reduced NAD
glycolysis. during this reaction.
a CO2
The product of the oxidative decarboxylation reaction is an acetyl group (meaning
b lactate a 2-carbon fragment). This acetyl group is then combined with a coenzyme called
c reduced NAD coenzyme A, forming acetyl coenzyme A.
d glycogen
NAD reduced NAD
e ATP
f NAD
pyruvate acetyl CoA
g pyruvate
h glucose
coenzyme A (CoA) CO2
The production of acetyl coenzyme A from pyruvate is known as the link reaction
because it connects glycolysis to the reactions of the Krebs cycle, which now follow.
diffusion from the cytosol

into the mitochondrion
pyruvate
(3-carbon)
NAD
the link reaction
reduced coenzyme A
CO2 NAD
acetyl coenzyme A
(2-carbon)
coenzyme A
oxaloacetate
citrate
(4 carbon) (6-carbon)
reduced NAD
Krebs CO2
cycle
NAD
reduced FAD (also known as the citric acid cycle)
FAD CO2
reduced NAD
5-carbon
NAD acid (α
ketoglutarate) NAD
ATP
produced ADP reduced NAD
at the
substrate level
There are several other organic acid intermediates in the cycle not shown here
▲ Figure 12.9 The link reaction and Krebs cycle: a summary
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In the Krebs cycle (Figure 12.9), the acetyl coenzyme A enters by reacting with a
oxaloacetate (a 4-carbon organic acid). The products of this reaction are a citrate (a 6-carbon
12 acid) and, of course, coenzyme A. This latter, on release, is reused in the link reaction.
The Krebs cycle is named after Hans Krebs who led the team that discovered it. It is also
sometimes referred to as the citric acid cycle, after the first intermediate acid formed.
Next, the citrate is converted back to oxaloacetate (an acceptor molecule, in effect) by a
series of reactions. This is why Krebs is called a ‘cycle’. These are the changes.
» Two molecules of carbon dioxide are given off, in separate decarboxylation reactions.
» A molecule of ATP is formed, as part of one of the reactions of the cycle. As is the
case with glycolysis, this ATP synthesis is at substrate level.

» Three molecules of reduced NAD are formed in dehydrogenation reactions.
» One molecule of another hydrogen accepter, FAD (flavin adenine dinucleotide), is
reduced. (NAD is the chief hydrogen-carrying coenzyme of respiration but FAD is
another coenzyme with this role in the Krebs cycle.)
Question Finally, remember that glucose was converted to two molecules of pyruvate in the
glycolysis phase. This means that the whole Krebs cycle sequence of reactions ‘turns’
7 Outline the types of twice for every molecule of glucose that is metabolised by aerobic respiration.
reaction catalysed by
We are now in a position to summarise the changes to the molecule of glucose that
a dehydrogenases
occurred in the reactions of glycolysis, the link reaction and the Krebs cycle. The products
b decarboxylases. formed during glycolysis and two turns of the Krebs cycle are shown in Table 12.1.
Products
Stage CO2 ATP reduced NAD reduced FAD
Glycolysis 0 2 2 0
Link reaction 2 0 2 0
Krebs cycle 4 2 6 2
Totals 6 4 10 2
Table 12.1 Net products of aerobic respiration per molecule of glucose at the end of the
Krebs cycle
The electron transport chain and oxidative phosphorylation

We have seen that the removal of pairs of hydrogen atoms from various intermediates of
the respiratory pathway is a feature of several of the steps in glycolysis, the link reaction
and the Krebs cycle.
Can you locate these points in Figures 12.8 and 12.9 now?
You can see that, at most of these events, NAD is converted to reduced NAD. However,
at one point in the Krebs cycle, an alternative hydrogen-acceptor coenzyme (known as
FAD) is reduced.
In this final stage of aerobic respiration, the hydrogen atoms (or their electrons) are
transported along a series of carriers, from the reduced NAD (or FAD), to be combined
with oxygen to form water. Hence the role of oxygen in this process is that of the final
electron acceptor. Note that this final reaction to form water only occurs after the
energy level has been lowered by a series of transfers between carriers, bringing about
the gradual transfer of energy shown in Figure 12.10.
The ‘carriers’ (they are conjugated proteins – page 52) are located in the inner membrane
of the mitochondria. These carriers occur in highly ordered sequences, each consisting
of hydrogen acceptors and electron carriers next to a final enzyme, ATP synthase
(known for short as ATPase). The location and physical structure of these systems are
illustrated in Figure 12.11.
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high energy electrons 1
/2O2
and H+ ions released
12
NAD+ 2H+ 2H+ H2O
oxygen atom
combines with
– – electrons and
2e 2e
hydrogen ions
to form water
12.2 Respiration
reduced NAD
from glycolysis
and the water formed
Krebs cycle in respiration,
Figure 12.10 The electrons passed from energy transferred
e.g. from the
electron transport carrier to carrier and used to
respiration of
chain and oxidative make ATP
food molecules,
phosphorylation: a when reduced FAD is oxidised, 2.5 ADP + 3Pi 2.5 ATP is called
only 1.5 molecules of ATP are formed metabolic water
summary
Question As electrons are passed between the carriers in the electron transfer chain, energy is
released. The energy is transferred to ADP and P i, forming ATP. The energy can then
8 Distinguish between be used by the cell.
the following pairs.
Normally, for every molecule of reduced NAD that is oxidised (that is, for every pair
a substrate and
intermediate of hydrogens) approximately three molecules of ATP are produced.
b glycolysis and the Theoretically at least, the total yield from aerobic respiration is about 38 molecules of
Krebs cycle ATP per molecule of glucose respired. In practice, it is less than that, probably about
c oxidation and 32 molecules of ATP.
reduction
How energy transfer and ATP synthesis are brought about
Firstly, we need to recognise that the inner membrane of the mitochondria (in which the
electron carriers are located) is a barrier to the movement of ions and electrons. Hydrogen
ions (protons) can get across but they have to be pumped, using energy. And once they
have been moved from the inner matrix of the mitochondrion to the tiny space between
the inner and outer membranes they are trapped there – temporarily, as it turns out.
It is the carrier proteins (a sequence of hydrogen carriers and electron carriers) that
use the energy of oxidation at several steps along the way, to pump the protons into
the inter-membrane space. Here, if they accumulate, they cause the pH to drop.
It is because the inner mitochondrial membrane is largely impermeable to ions that
a significant gradient in hydrogen ion concentration builds up across the inner
membrane, generating a potential difference across the membrane. This represents a
store of potential energy.
Then the protons are allowed to flow back into the matrix at particular points. These
points are ATP synthase molecules, each of which has a tiny channel. Note that this
enzyme occurs in the inner mitochondrial membrane, right besides each electron
transport chain. As the protons flow down their concentration gradient through the
channel in the enzyme, the energy is transferred to the synthesis of ATP from ADP
and P i. The reaction is catalysed by the ATP synthase (Figure 12.11, overleaf).
This process by which ATP is generated has become known as chemiosmosis. It
was a biochemist, Peter Mitchell, who suggested the chemiosmotic theory. This was
in 1961. His hypothesis was not generally accepted for some years but, about two
decades later, he was awarded a Nobel Prize for his discovery. Today there is a great
deal of evidence for the occurrence of chemiosmosis. We can describe it as a correct
hypothesis. So the word ‘theory’ in its title is used in its broadest sense – as an
accepted concept.
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stereogram of a mitochondrion, cut open outer membrane
12 to show the inner membrane and cristae

inner membrane
matrix
cristae
proteins of the proteins are
electron transport pumps that
chain transport H+
outer
mitochondrial
membrane
+ +
H+ H H+ H H
+
inter-membrane H+ H+ + H+ H+ hydrogen ions
H+ H H+ H+ H+ H+
space H+ H+ H+ H+ H+ (protons) accumulate
+ + +
H H H here creating a
inner potential difference
mitochondrial 2e– 2e– across the membrane
membrane 2e–
2e–
2e– oxidase proton channel
matrix of H+ enzyme
mitochondrion H+
1
NAD+ 2H+ + –2 O2
ATPase
reduced
NAD
H2O
ADP + Pi ATP
dehydrogenase
enzyme ATP synthesis coupled with proton H +
flow down concentration gradient
▲ Figure 12.11 ATP synthesis – Mitchell’s chemiosmotic theory
How ATP supports useful work in cells and organisms

We have noted that organisms need energy for many reasons, including:
» driving anabolic reactions
» the active transport of molecules and ions across membranes
» movement
» the maintenance of body temperature, where this occurs.
ATP is the chief source of free energy sustaining the metabolism and these activities of
cells and organisms (although it is not the form in which energy is stored long term).
How does the energy of ATP bring about such useful work in cells and organisms?
Question We have seen that ATP is formed from adenosine diphosphate (ADP) and a phosphate
9 State the most ion (Pi) by transfer of energy during respiration (Figure 12.3, page 242). Then, in the
common long-term presence of enzymes, ATP is involved in energy-requiring reactions. The free energy
energy store made available when ATP is formed from ADP and a phosphate ion is approximately
30–34 kJ mol–1. Some of this energy is lost as heat in the reaction, but much is
a in human cells
made available – more than sufficient to drive a typical energy-requiring reaction of
b in plant cells. metabolism. ATP typically reacts with other metabolites and forms phosphorylated
intermediates, making them more reactive in the process. The phosphate groups
are released later, so both ADP and phosphate ions become available for reuse as
metabolism continues.
Consequently, there is a huge turnover of ATP molecules in the cell cytoplasm
including in many organelles. ATP is used up very quickly after it has been formed from
respiratory substrates. Even while in a mainly resting state, the human body produces
and consumes about 40 kg of ATP in 24 hours. If we switch to very strenuous activity
about 0.5 kg of ATP is required every minute.
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EXTENSION
Case studies of ATP ‘at work’
12
1 An example of an anabolic reaction of metabolism ‘driven’ by ATP is the
manufacture of proteins in the ribosomes. Each amino acid used to build up the
primary structure of the protein is first attached to a specific molecule of transfer
RNA. ATP is required for this ‘activation’ reaction (Figure 6.14, page 134).
2 ATP also reacts directly with protein pumps in membranes, so providing the energy
needed to change the shape or activate the protein and so move ions and other
12.2 Respiration
metabolites across cell membranes which would otherwise block their movement. The
movement of a single substance is illustrated in Figure 4.23 (page 99). The sodium–
potassium pump is shown in Figure 4.24.
3 Sometimes ATP reacts with water (a hydrolysis reaction) and is converted to ADP
and a phosphate ion. For example, direct hydrolysis of the terminal phosphate
groups like this happen in muscle contraction.
Muscles that cause locomotion, skeletal muscle, consist of bundles of muscle fibres.
These fibres are long multinucleate cells that are able to shorten to half or even a third
of the relaxed or ‘resting’ length. The whole muscle fibre has a ‘stripy’ appearance.
This is due to an interlocking arrangement of two types of protein filaments, made of
the proteins myosin and actin.
electron micrograph of LS through part of a

skeletal muscle fibre, HP (×20 000)
mitochondria
sarcomere relaxed
+ sarcoplasmic
reticulum thin filament = actin thick filament = myosin
individual
myofibril
change in a single sarcomere in relaxed and contracted myofibril
Muscles contract as the actin and myosin filaments slide

between each other, shortening each sarcomere.
contracted
interpretive drawing of the thick filaments (myosin)
and thin filaments (actin)
actin
myosin
bulbous heads of myosin

filaments (ATP reacts here)
sarcomere
▲ Figure 12.12 The ultrastructure of a muscle fibre and contraction of a single sarcomere
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12 Look at Figure 12.12 now so that you can understand where ATP operates to bring about
muscle contraction.
Skeletal muscle contracts when the actin and myosin filaments slide past each other
in a series of steps, sometimes described as a ‘ratchet mechanism’. A great deal
of ATP is used in the contraction process. This cycle is repeated many times per
second, with thousands of m yosin heads working along each myofibril. ATP is used
up rapidly and the muscle may shorten by about 50 per cent of its relaxed length.
4 Another significant application of the energy transferred in respiration concerns

body temperature. The major source of heat in mammals (and in birds – both
groups of vertebrate which regulate their body temperature) is as a waste product
of the biochemical reactions of metabolism. Heat is then distributed by the blood
circulation.
The organs of the body vary greatly in the amount of heat they yield. For example,
the liver is extremely active metabolically, but most of its metabolic reactions require
an input of energy (they are endergonic reactions) and little energy is lost as heat.
Mostly, the liver is thermally neutral.
When at rest, the bulk of our body heat comes from other abdominal organs,
mainly from the heart and kidneys, but also from the lungs and brain (which, like a
computer central processing unit, needs to be kept cool). Under resting conditions,
the skeleton, muscles and skin, which make up over 90 per cent of the body mass,
produce less than 30 per cent of the body heat (Figure 12.13). Of course, in times of
intense physical activity, the skeletal muscles generate a great deal of heat as a waste
product of respiration and contraction.
organ mass heat

(as % of the production
total body at rest (as %
mass) of the total)
core organs of
abdomen
(mainly kidneys
and heart)
+
lungs
+
brain
Question skin
+
10 What does it mean muscles
+
when we say most skeleton
reactions in liver
cells are endergonic? ▲ Figure 12.13 Heat production in the
body at rest
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The site of cell respiration – structure in relation to function
The location of the stages of cellular respiration are summarised in Figure 12.14. You
can see that, once pyruvate has been formed from glucose in the cytosol, the remainder 12
of the pathway of aerobic respiration is located in the mitochondria. The relationship
between structure and function in this organelle is summarised in Table 12.2.
the enzymes of the link reaction cytoplasm

ATP movement by
and the Krebs cycle are located in
facilitated diffusion
the matrix
12.2 Respiration
the enzymes of glycolysis ADP
are located in the cytosol CO2 + Pi
H2O
glycolysis ATP
pyruvate hydrogen
acceptors ADP
glucose pyruvate breakdown
+ Pi
reduced ATP pyruvate
NAD reduced sites of oxidation of
hydrogen hydrogen acceptors
acceptors (water formation)
mitochondrion
outer membrane and ATP synthesis
inner membrane
cristae O2
CO2
▲ Figure 12.14 The location of the stages of cellular respiration
Structure Function
External double Permeable to pyruvate, CO2, O2, NAD and reduced NAD
membrane
Matrix Site of the enzymes of the link reaction and the Krebs cycle
Inner membrane • Surface area greatly increased by intucking to form cristae –
since the electron transport chain and ATP synthase enzymes
are housed here, opportunities for ATP synthesis are enhanced
• Impermeable to hydrogen ions (protons) – allowing the
formation of a potential difference between the inter-
membrane space and the matrix
Intermembrane space Relatively tiny space – allowing the accumulation of hydrogen
ions (protons) there to generate a large potential difference
with the matrix, making phosphorylation possible
▲ Table 12.2 Mitochondrial structure in relation to function
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EXTENSION
12 Respiration as a source of intermediates
Question We have seen that the main role of respiration is to provide a pool of ATP, and that
11 State which stages in this is used to drive the endergonic reactions of synthesis – among other things.
cellular respiration But the compounds of the glycolysis pathway and the Krebs cycle (respiratory
occur whether or not intermediates) may also serve as the starting points of synthesis of other metabolites
oxygen is available to needed in the cells and tissues of the organism. These include polysaccharides like
cells. starch and cellulose; glycerol and fatty acids; and many others.
Redox indicators
Dehydrogenases are enzymes involved in respiration, including glycolysis and the Krebs
cycle. They are present in biological material that can be used as the enzyme source,
such as actively respiring yeast culture and germinating seeds. Dehydrogenases catalyse
the oxidation of a substrate by removing hydrogen and transferring the hydrogen atoms
to coenzymes. Their activity can be detected by using redox indicators (hydrogen
acceptors), which change colour on reduction.
Commonly used redox indicators are methylene blue, which becomes colourless when
reduced, dichlorophenolindophenol (DCPIP), which is blue and turns colourless when
reduced, and tetrazolium chloride, which changes from pink to colourless.
Investigating factors that affect the rate of respiration in yeast

The effect of temperature on the rate of respiration of a suspension of yeast cells can be
investigated using a solution of methylene blue. Methylene blue is a redox indicator, as
discussed above: in solution it is blue when in an oxidised state but turns colourless if
exposed to a reducing agent.
Identical yeast suspensions in test tubes are required, as shown in Figure 12.15. The
layer of oil prevents oxygen from the air dissolving in the yeast suspension. In these
conditions, yeast respires anaerobically. The oil also prevents colourless methylene blue
solution becoming re-oxidised and turning blue again. Using simple water baths at a
range of appropriate temperatures, the time taken for tubes at each temperature to turn
colourless is measured and recorded. Typical results of investigations of temperature and
respiration rate are shown in Figure 12.21.
Can you explain the events and changes in the tubes as methylene blue becomes colourless?
Question water baths in a range of temperatures,

e.g. at 20, 25, 30, 35, 40 and 50°C
12 Detail what changes
are required to this oil
experiment in order
to investigate the active yeast stopclock
effect of substrate suspension
with methylene
concentration on the blue solution
rate of respiration.
▲ Figure 12.15 An investigation of the rate of
respiration in yeast
The variables in this investigation are shown in Table 12.3.
Controlled variables The amount and concentration of the yeast suspension

The volume of oil and methylene blue solution
Independent variable The range of temperatures
Dependent variable The time taken for decolourisation of the methylene blue
▲ Table 12.3
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Anaerobic respiration
Many organisms are able to respire in the absence of oxygen, at least for a short time.
They do so by a process called fermentation or anaerobic respiration. Some tissues in an 12
organism may respire anaerobically, too, when deprived of sufficient oxygen (see below).
In the absence of oxygen, flowering plants may respire by alcoholic fermentation, for
example, the cells of roots in waterlogged soil. Many species of yeast (Saccharomyces)
respire anaerobically (some do so even in the presence of oxygen). The products are
ethanol and carbon dioxide. Alcoholic fermentation of yeast has been exploited by
humans in wine and beer production for many thousands of years.
12.2 Respiration
glucose S ethanol 1 carbon dioxide 1 energy
C6H12O6 S 2CH3CH2OH 1 2CO2 1 energy
Incidentally, the respiratory quotient for anaerobic respiration by alcoholic
fermentation cannot be calculated since no oxygen is taken in. However, if some
respiration in a tissue is aerobic then a small amount of oxygen will be absorbed. The
respiratory quotient will be high, but less than 2. Generally, tissues with high respiratory
quotient values (RQs well above 1) indicate that some anaerobic respiration is occurring.
Vertebrate muscle is an example of a tissue that can respire anaerobically, but only when
the demand for energy for contractions is very great and cannot be fully met by aerobic
respiration. It is lactate fermentation that occurs here. The sole waste product is lactate.
Question glucose S lactate 1 energy
13 Name two products C6H12O6 S 2CH3CHOHCOOH 1 energy
of anaerobic Once again, these equations are balance sheets of the inputs (raw materials) and the
respiration in
output (products) of cellular respiration. They tell us nothing about the separate steps
muscle.
involved, each catalysed by a specific enzyme. They do not mention pyruvate, for example.
The pathways of anaerobic respiration

The respiratory pathways of alcoholic and lactate fermentation are shown in
Figure 12.16. When oxygen is not available, glycolysis continues and pyruvate
accumulates, at least initially. However, the Krebs cycle and oxidative phosphorylation
cannot take place because the aerobic oxidation of reduced NAD is now blocked. In a
tissue in which reserves of oxidised NAD have run out, glycolysis would cease.
How is the supply of pyruvate maintained in cells in the absence of oxygen?
In fermentation, reduced NAD is oxidised in other reactions. In effect, oxygen is replaced
as the hydrogen acceptor. In alcoholic fermentation, ethanal is the hydrogen acceptor, and
in lactate fermentation, pyruvate is the hydrogen acceptor. You can see this in Figure 12.16.
Now, glycolysis can continue in the absence of oxygen. However, the total energy yield
in terms of ATP generated in both alcoholic and lactate fermentation is limited to the net
two molecules of ATP generated in glycolysis per molecule of glucose respired.
2× 2×
glucose three-carbon pyruvate 6CO2 + 6H2O (aerobic
phosphorylated respiration
sugar 2 × NAD pathway)
net gain of reduced NAD

2 × ATP
2× CO2
2 × ethanal
Here ethanal is the Here pyruvate is the
acceptor for reduced reduced NAD reduced NAD acceptor for reduced
NAD. alcohol dehydrogenase lactate dehydrogenase NAD.
Figure 12.16 2 × NAD 2 × NAD
The respiratory
pathways of 2 × ethanol 2 × lactate
anaerobic
alcoholic fermentation lactate fermentation
respiration
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Anaerobic respiration is less efficient than aerobic respiration
12 Anaerobic respiration is wasteful of respiratory substrate. The useful product of

fermentation is a tiny quantity of ATP. This is minimal when compared with the yield
of ATP from aerobic respiration of the same quantity of respiratory substrate. Also, the
waste product, ethanol or lactate, contains much unused chemical energy. In fact, both
lactate and ethanol are energy-rich molecules. The energy in these molecules may be
used later, however. For example, in humans, lactate is transported to the liver and later
metabolised aerobically.
Energy yields of cellular respiration are compared in Table 12.4. You do not need to
memorise the details here, but give careful attention to two points:
» the limited yield in terms of molecules of ATP generated per molecule of glucose
respired by anaerobic compared with the yield from aerobic respiration
» the limited yield from substrate-level phosphorylation compared with the yield
from oxidative phosphorylation.
Yield from each molecule of glucose respired

Aerobic respiration Anaerobic respiration
Reduced NAD ATP Reduced NAD ATP
Stage (or FAD)
Glycolysis 2 2 reduced NAD 2
(net production (re-oxidised (net production
at the substrate during at the substrate
level) fermentation) level)
2 reduced NAD 2 × 2.5 = 5
(produced
by oxidative
phosphorylation)
Link 2 reduced NAD 2 × 2.5 = 5
reaction (produced
by oxidative
phosphorylation)
Krebs 2
cycle (net production
at the substrate
level)
6 reduced NAD 6 × 2.5 = 15
(produced
by oxidative
phosphorylation)
2 reduced FAD 2 × 1.5 = 3
(produced
by oxidative
phosphorylation)
Totals 32 2
Table 12.4 Energy yield of aerobic and anaerobic cellular respiration compared
Lactate and ethanol are harmful to organisms (in different ways) if they accumulate
in quantity. However, organisms may be able to tap the energy locked up in the waste
products of fermentation by converting them back to sugar, which can then be respired.
For example, as a result of prolonged, very strenuous exercise, lactate builds up in
the muscles. Eventually this lactate is carried in the blood stream to the liver. Here
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the lactate is converted back to glucose in the liver. This process requires energy from
respiration, too, and therefore requires extra oxygen. The oxygen needed to remove the
lactate is called the oxygen debt. 12
EXTENSION
Question
A few organisms respire only in the absence of oxygen. One is the tetanus bacillus
14 Can you suggest Clostridium tetani which causes the disease lockjaw. This bacterium is active in
a mechanism by oxygen-free environments rich in nutrients. These conditions occur in deep body
12.2 Respiration
which the absence of wounds. Otherwise the bacterium merely survives as resistant spores in the soil
oxygen in respiring or among the faeces of the lower gut of many animals. During growth (but not as
tissue might ‘switch a dormant ‘spore’), C. tetani produces toxins which, when released inside wounds,
off’ both the Krebs are carried around the body in the blood circulation, causes agonising muscular
cycle and oxidative spasms. Today, tetanus can be prevented by vaccination, supported by periodic
phosphorylation? booster injections.
Many species of yeast cannot metabolise ethanol; the energy locked up in ethanol
remains unavailable to the cell. This makes these species industrially useful organisms
in the production of ethanol. However, other yeast species can metabolise ethanol when
other respiratory substrates are used up.
Rice – a plant of waterlogged soils

Rice (Oryza sativa) is a semi-aquatic annual grass plant that flourishes in poorly
draining, silty soils. The plant was domesticated in south-west Asia about
12 000 years ago, which is much earlier than the first records of cultivated wheat
(in the Fertile Crescent). If so, rice has certainly fed more people over a longer
period than any other crop. Today, rice is the staple for more than 60 per cent of the
world’s population.
Rice is adapted to grow with its roots submerged in water (Figure 12.17, overleaf).
Here the environment for root growth is deprived of oxygen. In fact, the mud here is
in a permanent anaerobic state because of the respiration of the saprotrophic bacteria
present. These bacteria live off the dead organic matter present and tend to consume all
the available oxygen in the process. At the same time, plant root growth requires oxygen
for aerobic respiration. All plants absorb ions from the soil solution in their roots by
active uptake (page 98). Here, too, the plant manufactures essential amino acids, which
it then transports all over the plant. So the roots are highly metabolically active and
require oxygen for aerobic respiration and ATP production. Meanwhile, in waterlogged
soils oxygen is virtually absent.
How is rice adapted to grow in these conditions?
Firstly, the ground tissue cells (parenchyma) that make up the bulk of the stems and
roots of all plants show a special adaptation in the rice plant. Here, the cells have huge,
interconnecting air spaces between them, particularly of the roots. This tissue is known
as aerenchyma tissue – you can see it in Figure 12.17. These spaces between cells aid
the diffusion of oxygen to the roots, growing deeply in the waterlogged soil, typically
5–10 cm below the water surface. In fact, the aerenchyma tissue of the rice stem and
root makes possible normal growth and metabolism of the root system, in anaerobic
conditions.
Secondly, the roots can and do respire anaerobically by alcoholic fermentation, when
necessary. The ethanol produced in the cells may be metabolised by enzymes present,
but the root cells of the rice plant have a higher tolerance than other cereals for
ethanol.
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paddy field culture of rice – planting out of rice seedlings
Question
12 15 List the features of
the rice plant that
enable it to survive
swamp conditions.
Annotate your list, so
that the value of the
adaptation is made
clear.
aerenchyma tissue
photomicrograph of stem in TS (×100)
leaf blades
with stomata
rice fruit
air enters plant

via stomata in
aerial parts of
plant by diffusion
circular leaf
scanning electron micrograph of root in TS (×100)
bases around
stem
stems
(several tillers)
rice plants grow 0.5–5.0 m

paddy field according to variety
water
mat roots
ordinary
roots
▲ Figure 12.17 The structure of mature rice plants, as vegetative growth gives way to fruit formation
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EXTENSION
12
A source of combined nitrogen for rice plants of the paddy field
Azolla is a tiny, aquatic fern that grows profusely in flooded paddy fields, for example, in China and Vietnam.
Living in cavities of the fern leaf is a species of a photosynthetic bacterium, Anabaena (known as Anabaena azollae).
This cyanobacterium is a nitrogen-fixing organism. The ammonium ions it forms in excess are shared with the
fern cells. When the fern dies and decays, the soil of the paddy field is fertilised with additional combined nitrogen
which also supports the growth of the rice plants and makes possible productive, intensive cultivation of rice.
Human agriculture has benefited from this relationship for centuries, long before plant nutrition or the importance
12.2 Respiration
of combined nitrogen was u nderstood.
side view Anabaena filaments enlarged

Azolla fern
surface view heterocysts – site
of N-fixation
leaf enlarged
study of effect on rice yields of adding different

amounts of Azolla to soil of paddy field
roots
upper lobe
tonnes per hectare

rice yield increase/
in section 0.2
0.1
lower lobe on
surface of water 0
photosynthetic
cells pockets containing
10 20 30 40 50 60
Anabaena filaments
fresh weight of Azolla/tonnes per hectare
▲ Figure 12.18 Azolla as a nitrogen-fixation factory for paddy field rice
Practical: Investigating the effect of temperature on

respiration rate of germinating seeds or small invertebrates
The rate of respiration of an organism tells us about its demand for energy. The more
active the organism, the higher its rate of respiration. By ‘respiration rate’ we mean the
uptake of oxygen per unit time. This can be measured by means of a respirometer. A
respirometer is a form of manometer because it detects change in pressure or volume of
a gas. So, respiration rates are investigated by manometry.
A simple respirometer is shown in Figure 12.19, overleaf. Respiration by an organism
trapped in the chamber changes the composition of the gas there, once the screw clip has
been closed. Soda lime, enclosed in the chamber, removes carbon dioxide gas as it is released
by the respiring organism. Consequently, only oxygen uptake should cause a change in
volume. The drop of coloured liquid in the attached capillary tube will move in response.
The change in the volume of the apparatus, due to oxygen uptake, can be estimated from
measurements of the movement in the manometric fluid during the experiment.
Can you think of problems that might arise in using this apparatus?
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screw clip (closed when small drop of
apparatus has been assembled, coloured liquid
12
before experiment begins)
capillary tube The liquid drop moves due

perforated metal to a fall in pressure as the
cage holds CO2 volume is reduced, e.g.
absorbent when CO2 given out is
(soda lime) absorbed by the soda
lime, and O2 is taken up
by the seeds.
germinating seeds But a change

in temperature or
clamp atmospheric pressure
stand might have the same
effect, and handling of the
apparatus may add heat
and change the readings.
▲ Figure 12.19 A simple respirometer
Question With a differential respirometer (Figure 12.20), the sources of error arising from the
simple manometer are eliminated by having a control chamber connected by a U-tube
16 In the respirometer manometer to the respirometer chamber. External temperature or pressure changes act
shown in Figure equally on both sides of the manometer and cancel out. In this apparatus, the volume of
12.20, explain gas absorbed per unit time is given by readings on the syringe.
how changes in
temperature or
pressure in the 4 after a fixed time, the syringe is adjusted
to level the fluid in the two arms of the
external environment manometer, and the volume of O2
are prevented from absorbed is read off on the syringe
interfering with the
measurement of graduated syringe
oxygen uptake by the
respiring organisms A clips A and B are closed B
in the apparatus.
hypodermic
needle
respirometer tube
control tube
(thermobarometer) water bath
1 the respiring organisms

glass beads (same give off CO2 and
volume as sample in absorb O2
respirometer tube)
soda lime pellets soda lime pellets

(CO2 absorbent) (CO2 absorbent)
U-tube manometer 2 CO2 is absorbed by

Any change in pressure or temperature during the soda lime
the experiment affects the respirometer tube 3 manometer fluid moves to the right
and the thermobarometer tube equally. due to the fall in pressure as
the volume is reduced by the
by uptake of oxygen
▲ Figure 12.20 A differential respirometer
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between 10 and 35çC above 40çC The differential respirometer is used with a water bath. By
the rate of respiration at the rate of respiration decreases repeating readings at a range of different temperatures, the
least doubles for every
10°C rise; this is typical
of a chemical reaction
with a rise in temperature,
owing to denaturation of the
enzymes at higher temperatures
effect of temperature on respiration can be measured. Data
such as that in Figure 12.21 can then be obtained with this
12
equipment.
relative respiration rate / arbitrary units
Why does temperature affect the rate of respiration?

The enzymes of respiration are proteins. All proteins are
denatured by higher temperatures, although the temperature
at which proteins are denatured varies widely. For example,
12.2 Respiration
some bacteria live successfully in hot springs where the water
temperature may approach that of boiling water.
From the graph in Figure 12.21 we can work out the
temperature at which significant denaturing of respiratory
0 10 20 30 40 50 enzymes in the organisms used in the experiment takes
temperature / °C
place. Below this, a rise in temperature causes the rate of
▲ Figure 12.21 The effect of temperature on the rate of respiration to increase. It is a feature of chemical reactions
respiration that their rate at least doubles for every 10°C rise in
temperature.
SUMMARY
» Respiration is a cellular process in which energy » Glycolysis occurs in the cytoplasm, but the Krebs
is transferred from nutrients, such as glucose, to cycle is located in the matrix of mitochondria and
the cellular machinery. Energy is required to do oxidative phosphorylation occurs on the inner
useful work, such as the transport of metabolites mitochondrial membrane including the cristae.
across membranes, the driving of anabolic » In anaerobic respiration, the products are either
reactions and to cause movements in organisms. lactate (in lactate fermentation, typically found in
» Aerobic respiration involves the complete vertebrate muscle) or ethanol and carbon dioxide
oxidation of glucose to carbon dioxide and water (in alcoholic fermentation, found in yeast and in
with the release of a large amount of energy. In plants under anaerobic conditions).
addition to hexose sugars, fats and proteins may » Anaerobic respiration is wasteful of respiratory
be used as respiratory substrates. Anaerobic substrate. It yields only a tiny quantity of ATP,
respiration involves the partial oxidation of glucose when compared with the yield of ATP from aerobic
with the release of only a small amount of energy. respiration of the same quantity of respiratory
» ATP is the universal energy currency molecule by substrate. The waste products, ethanol or lactate,
which energy is transferred to do useful work. ATP contain much unused chemical energy. They are
is a soluble molecule, formed in the mitochondria both energy-rich molecules.
but able to move into the cytosol by facilitated » The rate of aerobic respiration can be
diffusion. It diffuses freely about cells. measured manometrically, in a respirometer.
» The stages of aerobic respiration are: The respiratory quotient (RQ) is the ratio of the
— glycolysis, in which glucose is converted to volume of carbon dioxide produced to the volume
pyruvate of oxygen used, in a given time. The respiratory
— the link reaction, in which pyruvate is quotient is an indicator of the respiratory
converted to acetyl coenzyme A substrate.
— the Krebs cycle, in which acetyl coenzyme A » Plants show adaptations to different
is metabolised, carbon dioxide is given off and environments. The adaptations to swamp
NAD (or FAD) is reduced conditions by rice include extensive aerenchyma
— the electron transport chain and oxidative tissue, with continuous, interconnecting air
phosphorylation, in which reduced NAD (and spaces throughout stems, leaves and roots, and
reduced FAD) are oxidised and water is formed. physiological tolerance of ethanol by root cells.
Most of the ATP is produced during this stage.
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12 1 Chemiosmosis is the term used to describe the synthesis of ATP using a proton
gradient across a membrane in a mitochondrion or chloroplast. It was first
demonstrated by Peter Mitchell in 1961.
a In some of his experiments, Peter Mitchell used mitochondria that had been
isolated from cells.
• The mitochondria were kept in liquid, in glass dishes, to which ADP, Pi and
other substances were added.
• The temperature, pH and water potential were kept constant.
• After a period of time he checked for the presence of ATP.

The contents of some of the dishes are shown in the table below.
Complete the table using a tick () if ATP was produced and a cross (×) if no
ATP was produced. [2]
Dish contents ATP produced

mitochondria + ADP + Pi + acetyl CoA + oxygen
mitochondria + ADP + Pi + acetyl CoA
mitochondria + ADP + Pi + low concentration of protons (H+)
mitochondria + ADP + Pi + high concentration of protons (H+)
b Explain the consequences to a mitochondrion if the water potential of the liquid
in the dishes is higher than the water potential of the mitochondrial matrix. [2]
c State the specific role of oxygen in the mitochondrion. [1]
d Name the enzyme used to produce ATP in chemiosmosis. [1]
e Describe the role of the inner mitochondrial membrane (crista) in
chemiosmosis. [4]
[Total: 10]
(Cambridge International AS and A Level Biology 9700, Paper 43 Q6 Oct/Nov 2017)
2 a
For the stages of aerobic respiration listed below, identify the site of the
process and the chief products of each step.
Component of process of Location of the process Chief products
aerobic respiration in the eukaryotic cell
Glycolysis
Link reaction
Krebs cycle
Oxidative phosphorylation
[12]
b What do you understand by:
i decarboxylation [2]
ii dehydrogenation? [2]
[Total: 16]
3 a During respiration, exchange of substances takes place between the cytoplasm
and the mitochondria.
Complete the table to list three substances that enter the mitochondria
and three substances that leave the mitochondria. [3]
Substance that enters the Substance that leaves the

mitochondria mitochondria
1
2
3
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b Tripalmitin is a triglyceride. The chemical equation for the aerobic respiration
of tripalmitin is:
2C51H98O6 + 145O2 → 102CO2 + 98H2O 12
i Calculate the RQ value for tripalmitin.
Give your answer to 2 decimal places.
Show your working. [2]
ii Explain why the usual RQ value for respiration in humans is
between 0.7 and 1.0. [2]
[Total: 7]

(Cambridge International AS and A Level Biology 9700 Paper 42 Q7 b,d Feb/Mar 2016)
4 Outline and explain:
a the difference between substrate level phosphorylation and oxidative
phosphorylation,
b why aerobic respiration is described as more efficient than anaerobic
respiration,
c how reduced NAD is reoxidised in anaerobic respiration.
5 a Fig. 5.1 outlines some of the steps of glycolysis.
glucose
step 1
glucose 6-phosphate
step 2
fructose 6-phosphate
step 3
fructose 1,6 bisphosphate

step 4
triose triose
phosphate phosphate
step 5
pyruvate pyruvate
▲ Fig. 5.1
i State the precise location of glycolysis in the cell. [1]

ii With reference to Fig. 5.1:
state the steps where phosphorylation occurs [1]
state the step where oxidation occurs [1]
name the type of reaction by which ATP is made during step 5. [1]
b Some cancer cells have different metabolic requirements from normal cells.
These cancer cells obtain most of their ATP from glycolysis, even if oxygen is
available.
State how the glucose and oxygen requirements of these cancer cells differ
from normal cells. [2]
[Total: 6]
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A LEVEL
13 Photosynthesis
13 Photosynthesis
Photosynthesis is the energy Learning outcomes

transfer process that is the
basis of much of life on
Earth. It provides energy 13.1.1 describe the relationship between the structure of chloroplasts, as
directly or indirectly to all shown in diagrams and electron micrographs, and their function
other organisms in most 13.1.2 explain that energy transferred as ATP and reduced NADP from the
food chains. In eukaryotes, light-dependent stage is used during the light-independent stage (Calvin
the process occurs within cycle) of photosynthesis to produce complex organic molecules
chloroplasts.
13.1.3 state that within a chloroplast, the thylakoids (thylakoid membranes and
Candidates should apply
their knowledge of plant
thylakoid spaces), which occur in stacks called grana, are the site of the
cells from Cell structure light-dependent stage and the stroma is the site of the light-independent
(Topic 1) and leaf structure stage
from Transport in plants 13.1.4 describe the role of chloroplast pigments (chlorophyll a, chlorophyll b,
(Topic 7) while studying carotene and xanthophyll) in light absorption in thylakoids
photosynthesis. Various 13.1.5 interpret absorption spectra of chloroplast pigments and action spectra
environmental factors for photosynthesis
influence the rate at which
photosynthesis occurs.
13.1.6 describe and use chromatography to separate and identify chloroplast
The practical activities in pigments (reference should be made to Rf values in identification of
this topic give opportunities chloroplast pigments)
for candidates to plan 13.1.7 state that cyclic photophosphorylation and non-cyclic
investigations, analyse and photophosphorylation occur during the light-dependent stage of
interpret data and evaluate photosynthesis
experimental procedures 13.1.8 explain that in cyclic photophosphorylation: only photosystem I (PSI) is
and the quality of the data
involved, photoactivation of chlorophyll occurs, and ATP is synthesised
that they collect.
13.1.9 explain that in non-cyclic photophosphorylation: photosystem I (PSI) and
photosystem II (PSII) are both involved, photoactivation of chlorophyll
occurs, the oxygen-evolving complex catalyses the photolysis of water,
ATP and reduced NADP are synthesised
13.1.10 explain that during photophosphorylation: energetic electrons release
energy as they pass through the electron transport chain (details of
carriers are not expected), the released energy is used to transfer
protons across the thylakoid membrane, protons return to the stroma
from the thylakoid space by facilitated diffusion through ATP synthase,
providing energy for ATP synthesis (details of ATP synthase are not
expected)
13.1.11 outline the three main stages of the Calvin cycle: rubisco catalyses the
fixation of carbon dioxide by combination with a molecule of ribulose
bisphosphate (RuBP), a 5C compound, to yield two molecules of
glycerate 3-phosphate (GP), a 3C compound; GP is reduced to triose
phosphate (TP) in reactions involving reduced NADP and ATP; RuBP is
regenerated from TP in reactions that use ATP
13.1.12 state that Calvin cycle intermediates are used to produce other
molecules, limited to GP to produce some amino acids and TP to produce
carbohydrates, lipids and amino acids
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Starting points
★ All the stages of photosynthesis occur in the chloroplast. 13
★ Light energy absorbed by chloroplast pigments in the light dependent stage
of photosynthesis is used to drive the reactions of the light independent stage
that produce complex organic compounds.
★ Chromatography is used to identify chloroplast pigments and was also used
to identify the intermediates in the Calvin cycle.
13.1 Photosynthesis as an energy transfer process

Chloroplasts – the site of photosynthesis
Mitochondria are the site of many of the reactions of respiration, but chloroplasts are
the organelles where all the reactions of photosynthesis occur. Chloroplast are one of
the larger organelles found in plant cells, yet they typically measure only 4–10 μm long
and 2–3 μm wide. As a result, whilst a single chloroplast can be seen in outline by light
microscopy, for detail of fine structure electron microscopy is required.
Look at the electron micrograph of a chloroplast in Figure 1.19, page 19, now.
There is a double membrane around the chloroplast. The inner membrane intucks
at various points, forming a system of branching membranes, called thylakoid
membranes. These thylakoid membranes are organised into many flat, compact, disc-
shaped piles, called grana (singular: granum). Between the grana are loosely arranged
tubular membranes suspended in a watery matrix, called the stroma. Also present are
starch grains, lipid droplets and ribosomes. Chlorophyll pigments occur bound to the
membranes of the grana (Figure 13.1).
Chloroplast, structure in relation to function

We have seen that the grana are the site of the light-dependent reactions and the
stroma the site of the light-independent reactions of photosynthesis. Table 13.1 overleaf
identifies how the structure of the chloroplast facilitates these functions.
Examine Figure 13.1 and Table 13.1 and then answer Question 1.
starch grains
grana (stereogram)
lipid droplets
chloroplast (diagrammatic view) lamellae of the stroma
ribosomes
TEM of the granum showing stroma granum double

thylakoid membranes in which membrane
chlorophyll pigments are held
(×38000)
thylakoid membrane
of the grana
chlorophyll pigments are contained

in the grana, sandwiched between lipids
and proteins of the thylakoid membranes
▲ Figure 13.1 The structure of the chloroplast
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Questions 1 Draw a diagram of part of a chloroplast to show its structure as revealed by electron
13 microscopy. Annotate your diagram to indicate the adaptations of the chloroplast to
its functions.
2 Distinguish between the following:
a light-dependent reactions and light-independent reactions
b photolysis and photophosphorylation.
3 Deduce the significant difference between the starting materials and the end-
products of photosynthesis.
13 Photosynthesis
Structure of chloroplast Function or role

Double membrane bounding the chloroplast Contains the grana and stroma, and is
permeable to CO2, O2, ATP, sugars and other
products of photosynthesis
Photosystems with chlorophyll pigments Provide huge surface area for maximum
arranged on thylakoid membranes of grana light absorption
Thylakoid spaces within grana Restricted regions for accumulation of
protons and establishment of the gradient
Fluid stroma with loosely arranged thylakoid Site of all the enzymes of fixation,
membranes reduction and regeneration of acceptor
steps of light-independent reactions, and
many enzymes of the product synthesis
steps
▲ Table 13.1 Structure and function in chloroplasts
Photosynthesis as energy transfer

In photosynthesis, green plants use the energy of sunlight to produce organic molecules,
mostly sugars, from the inorganic raw materials carbon dioxide and water. Oxygen is
the waste product. Photosynthesis occurs in green plant cells – typically, in the leaves.
Here energy from light is trapped by chlorophyll pigments, present in chloroplasts.
This light energy is then transferred to energy in the chemical bonds of a range of
organic molecules, including sugars and ATP. We summarise photosynthesis in single
equations:
carbon dioxide 1 water 1 energy → glucose 1 oxygen
Question 6CO2 1 6H2O 1 energy → C6H12O6 1 6O2
4 What do we mean
by ‘anabolism’ and Compare this equation with that for aerobic respiration (page 249).
‘catabolism’? At first sight it seems that the one process is simply the reverse of the other. In fact these
equations are merely ‘balance sheets’ of the inputs and outputs. Photosynthesis and
respiration occur by different pathways with many enzymes unique to one or the other
pathway. And of course, photosynthesis is an anabolic process, whereas respiration is a
catabolic one.
The sugars produced in photosynthesis provide the carbon ‘skeletons’ for the synthesis
of all the metabolites the plant needs. We can say that green plants are ‘self-feeding’
(autotrophic nutrition). This type of nutrition contrasts with the ways animals and
other organisms get their nutrients. In fact, it is green plant nutrition that supports the
living world as a whole. Green plants are the source of nutrients for almost all other
organisms, directly or indirectly. In this topic we look at photosynthesis as an energy
transfer process.
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Photosynthesis – inorganic to organic carbon
The bulk of living things consist of the elements hydrogen, oxygen, carbon and
nitrogen. This is due to the large quantities of water they contain and because most 13
other compounds present consist of carbon combined with hydrogen and oxygen.
Compounds containing carbon combined with hydrogen are known as organic
compounds. At least two and a half million organic compounds are known – more than
the total of known compound made from all the other elements. This great diversity of
organic compounds has made possible the diversity of life as we know it.
However, carbon is also abundant on earth as the inorganic compounds – chiefly

carbon dioxide and carbonates. It is by the process of photosynthesis that inorganic
carbon is converted to organic carbon. Photosynthesis is a reduction–oxidation process.
In Topic 12 the idea of redox reactions was introduced (page 243).
reduction
Question
6CO2 1 6H2O 1 energy → C6H12O6 1 6O2
5 What colour does the
pigment chlorophyll oxidation
chiefly reflect or
transmit rather than A feature of oxidation and reduction is an energy change, for when reduction occurs
absorb? energy is absorbed. In photosynthesis it is solar light energy that is transferred to the
chemical energy of organic compounds. Photosynthesis is thus simultaneously a process
of energy transfer and a process by which inorganic carbon is converted to organic forms
and built up into living organisms.
Light as an energy source

the spectrum of
the spectrum of
Light is only part of the total electromagnetic radiation from the
electromagnetic
radiation
visible light Sun that reaches the Earth. When visible light itself is projected
violet
400 nm through a prism we see a continuous spectrum of light – a
gamma rays
10–10 rainbow of colours, from red to violet. These colours have different
10–8
blue wavelengths. The wavelengths of the electromagnetic radiation
X-rays
500 nm spectrum and of the components of light are shown in Figure 13.2.
10–8 Of course, not all the colours of the spectrum present in white
ultraviolet green
visible
light are absorbed equally by chlorophyll. In fact, one colour is
10–4
infrared 600 nm even transmitted (or reflected), rather than being absorbed.
(heat) yellow
10–2
microwaves orange Investigating chlorophyll

100
700 nm Some plant pigments are soluble in water but chlorophyll is not.
radio waves red While we cannot extract chlorophyll from leaves with water, it can
102
cm 750 nm
be extracted by dissolving in an organic solvent such as propanone
▲ Figure 13.2 The electromagnetic radiation (acetone). With this solvent, extraction of chlorophyll is fairly
spectrum and the spectrum of visible light straightforward (Figure 13.3, overleaf).
Chlorophyll as a mixture – introducing chromatography

Plant chlorophyll consists of a mixture of pigments, two of which are chlorophylls.
Question
Chromatography is the technique we use to separate components of mixtures,
6 In Figure 13.4 especially when working with small samples. It is an ideal technique for separating
(page 273), how Rf biologically active molecules since biochemists are often able to obtain only very small
values are calculated quantities.
is explained. Suggest
why it may be useful The process of chromatography involves a support medium known as the stationary
to know the Rf value phase. Often, this consists of absorptive paper (paper chromatography), powdered solid
of a component in a (column chromatography) or a thin film of dried solid (thin-layer chromatography).
mixture? The mixture to be separated is dissolved in a suitable solvent and then loaded on to the
stationary phase at a spot near to but not at one edge. Each drop is allowed to dry. The
loading and drying sequence is repeated several times.
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1 fresh leaves detatched 2 leaves finely cut and 3 about 20 cm3 of propanone
from plant placed in a mortar (acetone) added as solvent,
13 then ground up with

a small quantity of washed
and dried sand (as abrasive)
and the contents ground again
to produce a concentrated
chlorophyll extract
measuring cylinder
13 Photosynthesis
fresh green
leaves
5 tubes centrifuged to 6 extracted pigment solution combined

remove suspended organic and stored in the cold, in the dark,
4 solution decanted into two centrifuge tubes and matter (wall fragments, as chlorophylls are unstable molecules
contents adjusted to balance quantities starch grains, etc.) once removed from the grana
(chlorophyll solution bleaches in
glass direct sunlight)
rod
aluminium
foil
chlorophyll
solution
▲ Figure 13.3 Steps in the extraction of plant pigments
After that, in both paper chromatography and thin-layer chromatography, the lower
edge of the stationary phase is introduced into a suitable chromatography solvent,
known as the moving phase. This occurs in an enclosed space – a boiling tube or small
glass tank, for example. The solvent is allowed to travel through the stationary phase
by capillarity, passing through the loaded spot. As the solvent front moves up the
chromatogram, components of a mixture move at different rates. This is because they
have different solubilities in the solvent. Also, the components of the mixture being
separated interact with the material of the stationary phase to differing degrees.
Before the solvent front reaches the opposite end of the chromatogram, the process is
stopped. The level reached by the solvent front is marked. The chromatogram is then
dried. The positions of coloured components of a mixture are easily located (as in the
case of chlorophyll). The locations of any components that are not coloured have to be
identified; various techniques are available.
Look at the chromatogram in Figure 13.4. Green leaves contain a mixture of
photosynthetic pigments. These include two types of chlorophyll, known as
chlorophyll a and chlorophyll b. The others pigments belong to a group of compounds
called carotenoids. Incidentally, larger samples of these individual pigments can be
obtained by column chromatography, for example. Such samples may be large enough to
investigate the properties of individual pigment molecules.
The chemistry of the chlorophylls is particularly important because they are directly
involved in the energy transfer processes in the chloroplasts. The structure of
chlorophyll is shown in Figure 13.5.
Look at the structure of chlorophyll now.
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paper chromatography bung
drop of pigment in process
13
solution ‘loaded’
chromatography
then dried
paper
capillary chromatogram
(process repeated
tube fitted into
several times)
slot in bung
chromatography
tank (saturated
with solvent
chlorophyll vapour)
spot

chromatogram
chlorophyll glass rods solvent front,

solution at point when loading spot
chromatography
run was stopped chromatography
Thin-layer chromatography Indentifying pigments by Rf values
carotene solvent
(a very quick separation)
The distance a particular substance
xanthophyll
Using: moves up the chromatogram relative
• thin-layer chromatography ‘plate’ to its solvent front is constant – this chlorophyll a –
(plastic film) pre-coated with value is known as the Rf value. blue-green
silica gel distance moved by substance chlorphyll b –
• chromatography ‘tank’ – flat- Rf = green
distance moved by solvent
bottomed tube with close-fitting
bung, containing shallow layer of The Rf value of
solvent chlorophyll a = 0.65
chlorophyll b = 0.45
(Method similar to paper
chromatography.) using a solvent of nine parts
petroleum ether to one part 90% origin (point where pigment mixture was
aqueous propanone (acetone). loaded and dried before separation)
▲ Figure 13.4 Preparing and running a chromatogram
The other carotenoid pigments – carotene and xanthophyll – are described as

accessory pigments. This is because they have the role of passing the light energy they
absorb on to chlorophyll, before it can be involved in photosynthesis.
The chlorophyll pigments occur in the grana, held in the lipids and proteins of the
thylakoid membranes. Chlorophyll is large – a ‘head and tail’ molecule, in fact. The
‘heads’ are hydrophilic and associate with proteins in the thylakoid membrane. The
‘tails’ are hydrophobic and associate with lipids in the thylakoid membranes. Also found
here with these pigments are the enzymes and electron-carrier molecules involved in
the steps of photosynthesis where light energy becomes chemical energy. We will look at
these shortly.
H2C chlorophylls a and b In the chloroplast, chlorophylls a and b

CH3 This is chlorophyll a; occur in the membranes of the grana – they
H3C chlorophyll b has an are sandwiched between the protein and
CH3 aldehyde group (–CHO) lipid layers of the membranes.
N N in the place of the CH3 .
Mg2+
N N
H3C CH3 chlorophyll has a
O conjugated protein ‘head’ head occurs
O containing magnesium associated
O with proteins
O O CH3 and
CH3 CH3 CH3
a hydrocarbon ‘tail’
CH3
tail is held
in the lipid layer
(and is folded)
▲ Figure 13.5 The structure of chlorophyll
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Questions The absorption and action spectra of chlorophyll
13 7 What feature of the

chlorophyll molecule
We have seen that light consists of a roughly equal mixture of all the visible
wavelengths, namely violet, blue, green, yellow, orange and red (Figure 13.2). Now
prevents it being the issue is, how much of each wavelength does chlorophyll absorb? We call this
soluble in water – information an absorption spectrum.
and why? The absorption spectra of chlorophyll pigments are obtained by measuring their
8 Why is absorption of violet, blue, green, yellow, orange and red light, in turn. The results are
chromatography a plotted as a graph showing the amount of light absorbed over the wavelength range of
useful technique for visible light, as shown in Figure 13.6a. You can see that chlorophyll absorbs blue and
13 Photosynthesis
the investigation of red light most strongly. Other wavelengths are absorbed less so or not at all. It is the
cell biochemistry? chemical structure of the chlorophyll molecule that causes absorption of the energy of
blue and red light.
The action spectrum of chlorophyll is the wavelengths of light that bring about
photosynthesis. This may be discovered by projecting different wavelengths, in turn and
for a unit of time, on aquatic green pondweed. This is carried out in an experimental
apparatus in which the rate of photosynthesis can be measured. The gas evolved by a
green plant in the light is largely oxygen, and the volume given off in a unit of time is a
measure of the rate of photosynthesis. Suitable apparatus is shown in Figure 13.15
(page 282), of which more later.
The rate of photosynthesis at different wavelengths may then be plotted on a graph on
the same scale as the absorption spectrum (Figure 13.6b). We have seen that blue and
red light are most strongly absorbed by chlorophyll. From the action spectrum we see
that it is these wave lengths that give the highest rates of photosynthesis.
Chlorophyll in solution versus chlorophyll in the chloroplast

The chlorophyll that has been extracted from leaves and dissolved in an organic solvent
still absorbs light. However, chlorophyll in solution cannot use light energy to make
sugar. This is because, in the extraction process, chlorophyll has been separated from
the membrane systems and enzymes that surround it in chloroplasts. These are also
essential for carrying out the biochemical steps of photosynthesis, as we shall now
discover.
results show that the

wavelengths of light absorbed
a) absorption spectrum b) action spectrum by photosynthetic pigments
measured using a spectrometer record of amount (largely red and blue) are
of photosynthesis occurring very similar to the wavelengths
at each wavelength that drive photosynthesis
amount of photosynthesis
amount of absorption
carotenoids
chlorophyll b chlorophyll a
400 500 600 700 400 500 600 700

wavelength/nm wavelength/nm
blue light red light
▲ Figure 13.6 Absorption and action spectra of chlorophyll pigments
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What happens in photosynthesis?
Fascinating ‘detective work’ by biochemists has shown us how photosynthesis works,
step by step. Not surprisingly, photosynthesis consists of a complex set of many 13
reactions taking place in chloroplasts in the light. However, these reactions divide
naturally into two stages.
It was investigations into the effect of temperature on the rate of photosynthesis that first
lead to the discovery that photosynthesis is a two-stage process. (We will return to the
issue of the effects of external factors that limit the rate of photosynthesis later in this
topic.) Meanwhile, the two inter-connected stages are:

» a light-dependent stage. This is a photochemical step which, like all photochemical
reactions, is largely unaffected by temperature. It involves the splitting of water
by light energy and the formation of reducing power (reduced hydrogen acceptor
molecules). Also energy transfer to ATP occurs and oxygen is released as a waste
product. This stage takes place in the thylakoid membranes and thylakoid spaces of
the grana in chloroplasts.
» a light-independent stage. This involves biochemical reactions which are catalysed
by enzymes and are highly temperature sensitive. These reactions are dependent
upon the supply of reduced hydrogen acceptor (reduced NADP) and ATP from the
light-dependent stage. Carbon dioxide is ‘fixed’ to form 3-carbon sugars and these
sugars are then used to synthesise other molecules. This stage takes place in the
stroma of chloroplasts.
These stages are summarised in outline, in the flow-diagram in Figure 13.7.

light energy
Photosynthesis in chloroplasts
Light-dependent stage Light-independent stage
in H2O CO2 in
light 2H (reducing power) enzymic
1 reaction ATP (energy currency) reactions
out O (CH2O) out
2 2
water split in the grana CO2 reduced in the stroma carbohydrate
▲ Figure 13.7 The two stages of photosynthesis: a summary
The light-dependent stage

In the light-dependent stage, light energy is used to split water (a step known as
photolysis). Hydrogen is then removed by a hydrogen acceptor, known as NADP
(nicotinamide adenine dinucleotide phosphate).
NADP is a molecule found in the organelles of plant cells. You will notice that NADP is
very similar to the coenzyme NAD of respiration, but it carries an additional phosphate
group, hence the acronym NADP (Figure 13.8, overleaf).
At the same time that reduced NADP is formed in the light-dependent stage, ATP is
generated from ADP and phosphate. Light energy is needed for this, too, of course.
This energy comes from photoactivated chlorophyll, and the process is known as
photophosphorylation. Also, oxygen is given off as a waste product of the light-
dependent stage.
This stage of photosynthesis occurs in the grana of the chloroplasts.
We will look at the structures involved (the photosystems) next, and then at the steps by
which it occurs.
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Figure 13.8 NADP and NADP NAD
NAD (nicotinamide adenine dinucleotide phosphate) (nicotinamide adenine dinucleotide)
13 H
H
CONH2
CONH2 adenine nicotinamide
adenine nicotinamide
N+
N+
ribose Pi Pi ribose
ribose Pi Pi ribose
Pi ‘rest of molecule’, recognised by enzymes

with which NAD is a coenzyme
action end (hydrogen
13 Photosynthesis
ion transport)
‘rest of molecule’
Mode of action
summary:
NAD+ + 2H+ + 2e− NADH + H+
changes at ‘action end’: H

H H
+ −
CONH2 + 2H + 2e CONH2 + H+
N+ N
The photosystems
Chlorophyll molecules do not occur haphazardly in the grana. Rather, they are grouped
together in structures called photosystems, held in the thylakoid membranes of the
grana (Figure 13.9).
In each photosystem, several hundred chlorophyll molecules plus accessory pigments
(carotene and xanthophyll) are arranged, grouped together. All these pigment molecules
harvest light energy, and they funnel the energy to a single chlorophyll molecule of the
photosystem. This molecule is known as the reaction centre. The different pigments
around the reaction centres absorb light energy of slightly different wavelengths, but all
‘feed into’ the reaction centre.
light absorbed
many pigment molecules

(chlorophyll and accessory
pigments such as carotene
and xanthophyll)
thylakoid energy funnelled

membrane to reaction centre
reaction centre of
chlorophyll a
(absorbing energy
at 700 nm – PS I,
or at 680 nm – PS II)
exited electrons
released from here
Figure 13.9 The and replaced by
structure of a low energy
(= ground-state)
photosystem electrons
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Now we also need to note that there are two types of photosystem present in the
thylakoid membranes of the grana. These differ in the wavelength of light that the
chlorophyll of the reaction centre absorbs: 13
» Photosystem I (PS I) has a reaction centre activated by light of wavelength 700 nm.
This reaction centre is also referred to as P700.
» Photosystem II (PS II) has a reaction centre activated by light of wavelength
680 nm. This reaction centre is also referred to as P680.
Photosystems I and II have differing roles, as we shall see shortly. However, they occur
grouped together in the thylakoid membranes of the grana, along with specific proteins,

many of which function as electron-carrier molecules.
How light energy is transferred

In the light, pigment molecules of the photosystems harvest light energy and funnel it
into a special chlorophyll molecule at the reaction centre of the photosystem.
We will now follow what happens next, starting with PS II, but remember that the two
photosystems operate simultaneously.
1 The light energy reaching the reaction centre of PS II activates a particular pair
of ground-state electrons in the special chlorophyll molecule there. These are
raised to an excited state and immediately captured by an electron acceptor in the
nearby chain of electron-carrier molecules (Figure 13.10). By the loss of electrons
the chlorophyll molecule is oxidised, causing it to immediately acquire electrons
from water. It is electrons in the ground state that fill the gap in the chlorophyll
molecule vacated by the excited electrons. By this process, the water molecule is split
(photolysis). The remainder of the water molecule is released as oxygen gas (two
oxygen atoms combine to form a molecule of oxygen) and hydrogen ions.
Meanwhile, the excited electrons are passed along a chain of electron carriers. As
this happens, the energy level of the excited electrons progressively falls back to
the ground state. However, the energy transferred from them as they flow along
causes the pumping of hydrogen ions (protons) from the chloroplast’s stroma into
the thylakoid spaces. Here the hydrogen ions accumulate – incidentally, causing
the pH to drop. The result is the creation of a proton gradient across the thylakoid
membrane – of which more shortly.
Light energy reaches the reaction centre of PS I at the same time. Here, light energy
again causes the ejection of particular ground-state electrons, raising them to an
excited state. These, too, are captured by an electron acceptor in the nearby chain of
electron-carrier molecules. Now there comes a difference.
2H+ pumped
high excited
across thylakoid
electrons
excited membrane
2e–
electrons from stroma
2e–
ch
ain
of reduced
ele
ctr NADP
on
ca
rri
energy er
s
level LIGHT
NADP
LIGHT PS I
H2O PS II (P700) 2e– ground-state
(P680) electrons
2H+ 2H+
2H+ hydrogen ions (protons) used to drive ATP
Figure 13.10 Z diagram ground-state 2e– + ½O2 + 2H+ accumulate in thylakoid space synthesis (see
low Figure 13.11)
showing the light- electrons
dependent stage of
photosynthesis passage of electrons from water to NADP
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part of a chloroplast Photosystems I and II work in tandem – receiving light energy, releasing excited
thylakoid electrons and replacing each lost electron by one in the ground state (PS II electrons
13
pigments, carriers
space come from split water; PS I electrons from PS II).
and enzymes of the
light-dependent
stage
Reduced NADP and ATP are required for CO2 fixation in
chloroplast the stroma. Through products of the light reaction (taking
membranes place in the thylakoid membrane), they are actually formed
granum on the stromal side, where they are required.
hydrogen ions
pumped across
membrane using PS I H+ H+
PS II
13 Photosynthesis
energy from ADP + Pi ATP

LIGHT excited electrons NADP+ reduced
LIGHT
NADP
2 electrons 2 electrons ATP synthase
in excited in excited (ATPase)
state H+ state
H+ ions flow
2e– e– e– H+ H+ stroma out through
channel in
ATPase
2e– 2e– causing catalysis
of ATP formation
H2O 2H+ + 2e– + 12 O2 energy for ATP

H+ H+
ground-state passage of electron synthesis comes
water- passage of electron + from electrochemical
electron via electron-carriers H H+
splitting via electron-carriers gradient in H+ ions
molecules hydrogen ions
molecules built up across
H+ H+ H+
H+ thylakoid H+ thylakoid thyllakoid membrane
space
compartment
thylakoid
lipid bilayer
membrane
of fluid mosaic
membranet
stroma
▲ Figure 13.11 The organisation of the thylakoid membrane
The gap vacated by these electrons in PS I is filled by electrons that have been
transferred from PS II. These have now fallen back to the ground state energy level.
Meanwhile, the excited electrons from PS I are passed along a short chain of electron
carrier molecules and their energy is transferred to form a molecule of reduced
NADP from NADP and hydrogen ions, in the stroma. In Figure 13.11 you can see
Questions that this occurs on the stromal side of the thylakoid membrane – an important point.
9 Both reduced 2 Finally, ATP is generated, a process known as photophosphorylation. This occurs by
NADP and ATP, chemiosmosis. (We previously met this same process in the mitochondria, page 253.)
products of the In the light-dependent stage, a gradient in hydrogen ions (protons) is built up
light-dependent stage between the thylakoid space and the stroma. These protons return from the
of photosynthesis, thylakoid space into the stroma through the pore in the ATP synthase enzyme
are formed on the molecules by facilitated diffusion, causing the synthesis of ATP from ADP and a
side of thylakoid phosphate ion. This enzyme is also part of the photosystem proteins present in the
membranes that face thylakoid membrane (Figure 13.11). In this way, synthesis of ATP is coupled to this
the stroma. Suggest movement of protons.
why this fact is
significant. We call this non-cyclic photophosphorylation for reasons that are clear when we
re-examine the Z diagram in Figure 13.10. Light energy is absorbed simultaneously
10 How is the gradient by both photosystems and excited electrons are emitted by both reaction centres. But
in protons between
the overall pathway of each pair of electrons is a progression. They pass from water,
the thylakoid space
first via PS II and associated electron acceptors and carriers to PS I and its associated
and the stroma
acceptors and carriers, to reduced NADP. In the process, the energy of the excited
generated?
electrons is used to build up the concentration of protons in the thylakoid space.
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Then, as the protons flow out via ATP synthase down their electrochemical gradient,
ATP is synthesised.
Incidentally, we should notice that ATP synthesis occurs on the stromal side of the 13
thylakoid membrane.
Photophosphorylation and the concentration of carbon dioxide

Sometimes, the concentration of carbon dioxide in a leaf in the light becomes very low.
(These conditions can occur – we will return to the subject of limiting conditions later
in this topic.) When this happens, fixation of carbon dioxide slows to a standstill. As

a result, reduced NADP accumulates in the stroma and NADP disappears. Without a
continuous supply of NADP, photosystems II and I are no longer able to operate together
as they do in non-cyclic photophosphorylation.
In this situation, another type of ATP formation may occur – known as cyclic
photophosphorylation. In cyclic photophosphorylation, excited electrons from the
reaction centre in PS I are able to ‘fall back’ to where they came from. However, the
route by which they do this is via the electron-carrier molecules that transfer energy
from these excited electrons and pump protons into the thylakoid space. The modified Z
diagram in Figure 13.12 illustrates this.
Consequently, some ATP synthesis by chemiosmosis is able to continue, despite the
absence of carbon dioxide. This type of photophosphorylation is called ‘cyclic’ because
the electrons have returned to the photosystem from which they originated. They are
‘recycled’ rather than used to form reduced NADP, but ATP is still generated.
Non-cyclic phosphorylation – a reminder Cyclic phosphorylation

• The normal flow of electrons is from water, via PS II and • Occurs when reduced NADP accumulates in the stroma – e.g. when CO2
electron carriers to PS I and electron carriers to NADP (see Figure 13.10). concentration is low and the light-independent stage is blocked.
• The excited electrons from PS II, as they lose the energy of the • Cyclic photophosphorylation results – excited electrons from PS I are
excited state, cause hydrogen ions (protons) to be pumped across into captured by electron acceptors serving PS II, and then returned to a ground
the thylakoid space. state (pumping protons as they go), to re-occupy their original space in PS I.
• The gradient in protons between thylakoid space and the stroma • The proton gradient between the thylakoid space and the stroma is
causes protons to flow through ATP synthase and generate ATP. maintained and ATP formation continues.
NADP
2e –
s out: ion
P run t
If NAD osphoryla reduced NADP
c li c ph
c y
ch 2e–
em non-cyclic
ios
ele mo
ctr sis 2e– photophosphorylation
ADP on alo
-ca ng
+ rrie
2H2O 2e –Pi rs
yst
em LIGHT
PS I
ATP 700 nm Key
4H+ + O2 2e– LIGHT = non-cyclic photophosphorylation
photolysis PS II = cyclic photophosphorylation
680 nm
▲ Figure 13.12 A comparison of light-dependent cyclic and non-cyclic photophosphorylation
The products of the light-dependent reactions and their role

Now because the sequence of reactions of non-cyclic photophosphorylation are repeated
again and again, at very great speed throughout every second of daylight, large amounts
of the products of the light-dependent reactions (ATP and reduced NADP) are formed.
However, ATP and reduced NADP do not accumulate. They are essential components
of steps in the light-independent reactions that occur in the surrounding stroma. As
a result, ADP, Pi and NADP are continuously released from the stroma in the light and
reused in the grana. We shall see why this is so, next.
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Questions The light-independent reactions
13 11 What are the
ultimate fates
In summary, in the light-independent stage, carbon dioxide is reduced to carbohydrate in
the stroma of the chloroplasts. It occurs in three steps of a cyclic process, now known as
of electrons the Calvin cycle, and requires a continuous supply of the products of the light reaction
displaced from the (Figure 13.13). The enzymes of the light-independent reactions are light activated.
reaction centre of In step 1 carbon dioxide, which readily diffuses into the chloroplast, is combined
photosystem I with an acceptor molecule in the presence of a special enzyme, ribulose bisphosphate
a in non-cyclic carboxylase (rubisco for short). The stroma is packed full of rubisco. This enzyme
photo- makes up the bulk of all the protein in a green plant – it is the most abundant enzyme
13 Photosynthesis
phosphorylation present in the living world. The acceptor molecule is a five-carbon sugar, ribulose
b in cyclic photo- bisphosphate (referred to as RuBP). Carbon dioxide is added in a process known as
phosphorylation? fixation. When one ‘carbon’ is added to five carbons should we not expect the product
12 In a school to have six carbons? In fact, two molecules of a three-carbon compound, glycerate-3-
laboratory phosphate (GP) are formed. GP is essentially an organic acid – it is not at the energy
demonstration of level of a sugar.
the Hill reaction In step 2 GP is then reduced to triose phosphate, a three-carbon sugar. This is a
(page 285), what
high-energy level product and the reactions are brought about by reduced NADP and
electron acceptor is
ATP. Reduced NADP and ATP are therefore essential for the formation of sugar in
used, and where do
photosynthesis.
the electrons come
from? In step 3 regeneration of the acceptor molecule occurs. For every six molecules
13 Many biologists are of triose phosphate formed, five are used to form three molecules of RuBP. In this
not surprised the conversion, energy from ATP is also required. From the other molecule of triose
enzyme rubisco is phosphate other compounds are synthesized. These include carbohydrates (sugars and
the most abundant starch, and sucrose for translocation in the phloem), lipids, and amino acids. In these
enzyme present in conversions energy from ATP is also required. How the products of photosynthesis
the living world? sustain the whole metabolism of the plant is summarised in Figure 13.14.
Suggest why.
chloroplast carbon
dioxide
granum stroma
NADP
reduced NADP
reduced
NADP ADP + Pi NADP
ATP
ATP
reduction
triose phosphate
glycerate ADP + P i
products from the 3-phosphate (GP)
light-dependent
stage C–C–C + C–C–C Calvin
2 × 3-carbon cycle
fixation compound
rubisco
product synthesis
(CO2-fixation +C
enzyme) a 1-carbon
ribulose compound lipids amino sugars starch
bisphosphate acids
change in carbon
C–C–C–C–C
skeletons
ADP + P i a 5-carbon
during fixation
compound
lipids amino sugars starch
ATP acids
regeneration translocated to rest

of acceptor of plant
▲ Figure 13.13 The reactions of the light-independent stage in situ

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the rest of
the plant oxygen from
sugars are translocated

in the phloem as sucrose
the air
13
oxygen
energy from sunlight the leaf carbon
triose doxide
photosynthesis phosphate
in chloroplasts O2 + triose respiration
carbon + water phosphate
dioxide in leaf cells ions energy

storage cellulose, and
oxygen diffuses carbohydrates, other wall-forming
carbon dioxide in air loss of water
into the fats and waxes compounds
vapour
atmosphere
vitamins,
. Ions are also carried to the leaves where much amino acid proteins, hormones
enzymes, and growth
. synthesis occurs.
Many vitamins are synthesised in the chloroplasts too.
ROOTS
cytoplasm factors
water
ions actively
absorbed
▲ Figure 13.14 Photosynthesis: its place in plant nutrition
EXTENSION
Finding the path of carbon in photosynthesis photosynthesis, from carbon dioxide to sugars and the
Radioactive carbon (carbon-14) became available for other products of photosynthesis.
biochemical investigations in 1945. One of the early A culture of Chlorella, a unicellular alga, was used in
applications was an investigation of photosynthetic these experiments, in place of mesophyll cells. This
carbon dioxide fixation. It was undertaken by was because they have similar photosynthesis and they
Melvin Calvin, James Bassham and Andy Benson in allow easy sampling. Samples of the photosynthesising
14
California. Carbon dioxide labelled with carbon-14 cells, taken at frequent intervals after a pulse of CO2
(14CO2) is taken up by the cells and is fixed into the had been given were harvested and analysed. The
products of photosynthesis in just the same way as intermediates that became progressively labelled with
unlabelled carbon dioxide (12CO2) is. It was then the carbon-14 were isolated by chromatography and
possible to discover the sequence of metabolites which then identified.
become labelled – in effect, the path of carbon in
EXTENSION
Chemosynthesis and water. Consequently, these organisms are known
Autotrophic organisms are ‘self-feeding’ organisms. as chemosynthetic. Two important examples of
They fall into two distinct groups, according to the chemosynthetic autotrophs that we meet elsewhere in
source of energy used to build carbon dioxide into this book are:
carbohydrates. » the nitrifying bacteria, that occur in the soil. These
One group, the photosynthetic organisms, use light microorganisms oxidise ammonium ions to nitrites
energy. We have focused on photosynthesis in this or nitrites to nitrates. Both of these reactions
topic. provide the bacteria with energy needed to synthesis
carbohydrates.
Another group of autotrophic organisms are unable to » the iron bacteria, which are sometimes used in
use light energy. Instead, a specific chemical reaction is industry in the extraction of metal from low-grade
catalysed in order to transfer the free energy required ores.
to synthesise organic compounds from carbon dioxide
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13.2 Investigation of limiting factors
13.2.1 state that light intensity, carbon dioxide concentration and temperature
are examples of limiting factors of photosynthesis
13.2.2 explain the effects of changes in light intensity, carbon dioxide
concentration and temperature on the rate of photosynthesis
13.2.3 describe and carry out investigations using redox indicators, including
13 Photosynthesis
DCPIP and methylene blue, and a suspension of chloroplasts to

determine the effects of light intensity and light wavelength on the rate of
photosynthesis
13.2.4 describe and carry out investigations using whole plants, including
aquatic plants, to determine the effects of light intensity, carbon dioxide
concentration and temperature on the rate of photosynthesis
Starting point
★ Environmental factors influence the rate of photosynthesis. Investigating
these shows how they can be managed in protected environments used in
crop production.
Question The environment and the rate of photosynthesis

The rate of photosynthesis can be measured in an aquatic plant, using a microburette –
14 A thermometer is
also called a photosynthometer (Figure 13.15). The experiment requires a freshly
not shown in the
apparatus in Figure cut shoot of aquatic green pondweed which, when inverted, produces a vigorous
13.15. Predict why stream of gas bubbles from the base. The bubbles tell us the pondweed is actively
one is required and photosynthesising. The pondweed is placed in a very dilute solution of sodium
state where it should hydrogencarbonate, which supplies the carbon dioxide (as hydrogencarbonate ions)
be placed. required by the plant for photosynthesis. The quantity of gas evolved in a given time is
measured by drawing the gas bubble that collects into the capillary tube and measuring
its length. This length is then converted to a volume.
Using this apparatus the effects of external conditions such as light intensity, carbon
dioxide concentration and temperature on the rate of photosynthesis have been
investigated.
Note: this experiment can be simulated on a computer.
plastic tube
syringe
stand
bubble of gas
heat being measured
trap
bubble
of gas
collecting end of
capillary tube
light Elodea capillary stop clock

tube
dilute hydrogencarbonate
solution
▲ Figure 13.15 Measuring the rate of photosynthesis with a microburette

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Light and carbon dioxide as limiting factors
Clearly, light is essential for photosynthesis. Green plant cells in the dark are unable to
photosynthesise at all; under this condition the only gas exchange by the leaf tissues is 13
the uptake of oxygen for aerobic respiration. Carbon dioxide is also lost.
As light starts to reach green cells, at dawn for example, photosynthesis starts, and
some oxygen is produced. Eventually the light intensity increases to the point where
oxygen production by photosynthesis is equal to oxygen consumption in respiration.
Now the leaf is neither an oxygen importer nor exporter. This point is known as the
compensation point (Figure 13.16).

O2
compensation point respiration
increasing CO2
uptake O2
CO2
photosynthesis
CO2
increasing CO2 photosynthesis faster than respiration;
evolution O2 concentration rises
What is happening in the leaf

as light becomes available –
and then the light intensity
increases? dark light
increasing light intensity
in darkness, a green plant as light intensity increases eventually, the compensation point
cannot photosynthesise but in the daylight, so does the is reached when all the CO2 produced
respiration continues rate of photosynthesis in respiration by the plant is reused in
photosynthesis, and there is no net
loss or gain in O2
O2
respiration
O2
respiration
CO2
photosynthesis
CO2
no photosynthesis; CO2 concentration rises rate of respiration and photosynthesis

equal; no exchange of gases with the environment
▲ Figure 13.16 Light intensity and the compensation point
Then, as the light intensity increases further, the rate of photosynthesis also increases;
the leaf becomes a net exporter of oxygen.
We can see the general effect of increasing light intensity on the rate of photosynthesis
in Figure 13.16. At low light intensities the rate of photosynthesis increases in
proportion to the increasing light. Here the low light intensity (i.e. the lack of sufficient
light) is limiting the rate of photosynthesis. Light is a factor limiting the rate of
photosynthesis under this condition.
However, as light intensity is raised further, a point is reached where increasing light
intensity produces no further effect on the rate of photosynthesis. Now some factor
other than light is limiting photosynthesis.
What may now be limiting the rate?
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The limiting factor at that point is disclosed when the investigation is repeated at either
higher light (Figure 13.17) or carbon dioxide concentrations, but not at the same time.
13 Look at this graph in Figure 13.17 now and follow the annotations.
Understanding this graph 3 Suddenly there is no further increase in photosynthesis

Read the axis labels (x + y axes) as light intensity is increased (light is no longer the limiting
and look at the shapes of the factor) – perhaps because the CO2 concentration is now insufficient?
curves. Then follow the points
(e.g. volume of O2 produced by a

experiment repeated at a
numbered 1 to 4.
given leaf area in unit time)

higher CO2 concentration
13 Photosynthesis
net photosynthesis
4 Yes! Because when the experiment is repeated at a
higher CO2 concentration, the rate of photosynthesis
rises until a higher light intensity is reached.
low CO2 concentration
2 Photosynthesis rate increases with

increasing light intensity (light is limiting).
1 Without light there

is no photosynthesis.
low high
light intensity
▲ Figure 13.17 The effect of light intensity on the rate of photosynthesis
carbon dioxide concentration as a limiting factor

high light intensity
The results of these earlier, physiological investigations fit well with
CO2 is not rate-limiting our current understanding. Photosynthesis is a biochemical process
rate of photosynthesis
involving a series of interconnected reactions (Figure 13.20). All

these reactions contribute to the overall rate of photosynthesis.
low light intensity However, at any one time, the rate of photosynthesis will be limited
what is now limiting the rate? by the slowest of these reactions – the overall rate will be limited by
the factor that is in shortest supply. This factor, whichever one it is,
is known as the limiting factor.
CO2 is rate-limiting
Clearly, a limited supply of either light (Figure 13.17) or carbon
dioxide (Figure 13.18) could determine the rate of photosynthesis,
0 low high since both of these are essential.
concentration of CO2 /arbitrary units
▲ Figure 13.18 The effect of carbon dioxide

Both light intensity and carbon dioxide concentration can be
concentration on photosynthesis limiting factors in photosynthesis.
5 at high light intensity temperature rise

The effect of temperature on the rate of photosynthesis
increases rate of photosynthesis The effect of temperature on the rate of photosynthesis, under
A controlled laboratory conditions, is especially informative. This
rate of photosynthesis/arbitrary units
4
is because, one effect of increasing temperature, say in the range
from 10°C to 30°C, depends upon light intensity. Under low light
3
intensities, a rise in temperature has little effect. Under higher
intensities, the rise in temperature increases the rate of photosynthesis
significantly. This relationship is shown in Figure 13.19.
2 at low intensity temperature
rise does not affect rate of How can this effect be explained?
photosynthesis
B
Under low light intensity, light is obviously the limiting factor.
1 Now a light-dependent reaction, like all photochemical events,
is temperature indifferent. In the same way, a light-independent
reaction (like all biochemical steps catalysed by enzymes) is highly
0 temperature sensitive.
0 10 20 30
temperature/°C
▲ Figure 13.19 The effect of temperature on the rate of photosynthesis

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light oxygen carbon dioxide
Question energy O2 CO2
15 a Suggest why we
should expect in chloroplasts
13
that high external ATP
temperatures grana + stroma
cause the rate of reduced
NADP CO2
photosynthesis light energy sugars built
to fall off very used to split water
H up by
(photolysis) reduction of
rapidly?

2H2O O2 + 4H carbon dioxide
b What may triose
effectively prevent phosphate
NADP
over-heating of sugars
+ starch
green leaves? ADP + Pi
water carbohydrates, lipids

and amino acids
▲ Figure 13.20 Photosynthesis: a summary
The graph in Figure 13.19 was interpreted as showing that photosynthesis is made up
of two sequential stages, a light-dependent stage and a light-independent stage. Later,
this idea was confirmed, once photosynthesis was investigated by entirely different,
biochemical techniques, including the use of chloroplasts isolated from a leaf, for
example.
Practical: Investigating the rate of photosynthesis using

an isolated chloroplast suspension – the Hill reaction
Introducing the Hill reaction
Chloroplasts can be isolated from green plant leaves and suspended in buffer solution
of the same concentration as the cytosol (an isotonic buffer), see Figure 13.21, overleaf.
If the suspended chloroplasts are undamaged, they function much as they do in the
intact leaf. These isolated chloroplasts can be used to investigate the splitting of water,
for example. However, this requires the natural electron-acceptor enzymes and electron-
carrier molecules to be present, or the substitution of an alternative.
In the research laboratory, a sensitive piece of apparatus called an oxygen electrode is
used to detect the oxygen given off by isolated chloroplasts.
In your laboratory, a hydrogen-acceptor dye that changes colour when it is reduced
is a practical alternative. The dye, DCPIP (dichlorophenolindophenol) is an example.
DCPIP does no harm when added to chloroplasts in a suitable buffer solution, but
changes colour from blue to a colourless state when it is reduced. The splitting of water
by light energy (photolysis) is the source of hydrogen that turns DCPIP colourless. The
photolysis of water and the reduction of the dye are represented by the equation:
2DCPIP 1 2H2O → 2DCPIPH2 1 O2
This demonstration is referred to as the Hill reaction after the research scientist
who first demonstrated this ‘reducing power’ of illuminated chloroplasts. It is a
demonstration of the light-dependent stage outside of the leaf.
Setting up reaction mixtures and collecting reliable data

Isolated chloroplasts are re-suspended in 0.1% phosphate buffer solution at pH 6.5.
With a chloroplast suspension to hand, the reaction mixtures listed in Table 13.2 can
be assembled in individual colorimeter tubes, adding the chloroplast suspension last
(all volumes in cm3), when ready to carry out the measurements. The measurements are
made in a colorimeter with green filter in place. Tubes 2, 3 and 4 are all control tubes.
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1 Chilled green leaf tissue 2 The homogenate is filtered through 3 The filtered homogenate
is ground up in a muslin (cheesecloth) to remove the is centrifuged at low speed
13 homogeniser (blender) larger debris (part ground cells)

centrifuge tubes with
de-veined homogenate filtered homogenate
leaves (cold)
centrifuge
grinding cheesecloth (8 layers) head (cold)
medium (cold) funnel
homogeniser centrifuge tube
centrifuge
filtered homogenate
motor base ice bucket motor
13 Photosynthesis
4 The heavier particles and the 5 The supernatant liquid 6 The high-speed centrifugation
larger organelles are precipitated; is re-centrifuged at high speed precipitates the lower-mass
the supernatant is decanted organelles as a pellet
centrifuge tubes with
supernatant suspension supernatant
supernatant (discarded)
chloroplast
pellet centrifuge
pellet
head (cold)
supernatant pipette
glass rod
centrifuge
pellet resuspending
motor re-suspended
medium (cold)
chloroplasts
combined
chloroplast
suspension
▲ Figure 13.21 Isolating intact chloroplasts by differential centrifugation
Tube Buffer DCPIP Distilled Chloroplast Treatment

(0.1%) (0.1% water suspension
sol)
1 8.0 0.2 0.0 0.5 Placed in the colorimeter and the
scale adjusted to read 0.7 on the
absorbance scale.
Then the tube removed, exposed
to bright light, and returned to the
colorimeter at 15 second intervals
until no further change in the
absorbance occurs.
This time is recorded.
2 8.0 0.2 0.0 0.5 Contents kept in complete darkness
(wrapped in aluminium foil) for
the same period of time that Tube
1 takes to show no further colour
change. Then the foil is removed
and the absorbance read in the
colorimeter, and also recorded.
3 8.0 0.2 0.5 0.0 These tubes are treated in the same
way as Tube 1, maintaining the
cycle of exposure and recording of
absorbance for the same period of
4 8.0 0.0 0.2 0.5
time it takes for Tube 1 to show no
further colour change.
▲ Table 13.2 Reaction mixtures

Discuss the results you anticipate with peers and your teacher, and then answer Question 16.
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Question 16 Given that a chloroplast suspension will decolourise a blue DCPIP solution in the
light, explain:
a why the steps to the chloroplast extraction were carried out in an ice-cold water
13
bath, where possible
b why, for the experiment itself (tubes in the light and the dark), the reaction
mixtures were allowed to warm to room temperature.
c why an isotonic buffer solution is used to re-suspend the chloroplasts, rather than
distilled water

d what colour change you anticipate in Tubes 1 and 2, if any
e what issues the control tubes (3 and 4) will resolve.
SUMMARY
» Photosynthesis is an energy transfer » Photosynthesis can be divided into two linked
process in which green plants manufacture stages.
carbohydrates from carbon dioxide and water, – A light-dependent stage occurs in the grana
using energy from sunlight. Oxygen is the waste and results in the formation of reduced NADP
product. Chloroplasts, the organelles in which and ATP. It involves the photolysis of water and
photosynthesis occurs, are chiefly found in the release of oxygen.
the mesophyll cells of the leaves, particularly – A light-independent stage occurs in the
the palisade mesophyll cells. Plants use the stroma and involves the fixing of carbon
products of photosynthesis to manufacture the dioxide to form trioses, using the products of
other carbohydrates, lipids, proteins and all other the light-dependent stage. Trioses are used in
metabolites, enzymes and pigments required. For a variety of biochemical reactions within the
this they require energy transferred by respiration chloroplast to form monosaccharides (glucose
and selected mineral ions, absorbed from the and fructose) that are converted to sucrose for
soil. Consequently, plant nutrition is described as translocation or to starch for storage. Other
autotrophic (self-feeding). reactions use minerals from the soil to form
» The leaf is the ‘factory’ for photosynthesis, with amino acids that are translocated and used for
palisade cells in positions to absorb maximum protein synthesis.
light. The cells are supplied with water from the » In green plants the volume of oxygen-enriched
xylem vessels, and with carbon dioxide from gas given off in the light is a measure of the
the air by diffusion through open stomata. The rate of photosynthesis. The volume of gas
products of photosynthesis are exported from the produced by aquatic plants under different
leaf in the sieve tubes in the phloem. conditions can be measured using a microburette
» Chloroplasts are enclosed by a double membrane. (photosynthometer).
The inner membrane intucks to form the » As photosynthesis consists of a number of
membrane systems of the chloroplast (thylakoid interconnected reactions, the slowest will
membranes). These are arranged in compact, determine the overall rate. The factor limiting its
disc-shaped piles called grana, around which are rate is then described as the limiting factor. A
loosely arranged thylakoid membranes of the limited supply of either carbon dioxide or light will
stroma. limit the overall rate of photosynthesis, since both
» Chlorophyll consists of a mixture of pigments, are essential for photosynthesis.
two of which are chlorophylls. They can be » The autotrophic nutrition of the green plant also
separated by chromatography. Measurements of sustains other living things, since other organisms
the absorption spectrum of chlorophyll and the feed on plants or plant products, directly or
action spectrum of photosynthesis show that it is indirectly.
the blue and red components of white light that
are selectively absorbed and are most effective in
bringing about photosynthesis.
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13 1 a F
ig. 1.1 shows the effect of temperature on the rate of photosynthesis of a plant
at low light intensity and at high light intensity.
high light
rate of photosynthesis
intensity
13 Photosynthesis
low light
intensity
0 5 10 15 20
temperature/°C
▲ Fig. 1.1
ith reference to Fig. 1.1, describe and explain the effect of temperature on the
W
rate of photosynthesis. [4]
b Fig. 1.2 shows an absorption spectrum for chloroplast pigments and a
photosynthetic action spectrum for the same plant.
absorption
absorbance or rate of
spectrum
photosynthesis
action
spectrum
400 500 600 700

wavelength of light/nm
▲ Fig. 1.2
i Distinguish between an absorption spectrum and an action spectrum. [2]

ii Explain why the two curves shown in Fig. 1.2 have similar shapes. [2]
c Describe the role in photosynthesis of an accessory pigment, such
as carotene. [2]
[Total: 10]
(Cambridge International AS and A Level Biology 9700, Paper 42 Q2 May/June 2016)
2 a B
y means of a large, fully labelled diagram, describe the structure of a
chloroplast, as disclosed by electron microscopy. [6]
b Annotate your diagram to identify the function or role of the structures you
have labelled. [4]
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c In investigations of the physiology and biochemistry of photosynthesis,
suspensions of single-celled algae (simple, photosynthetic organisms
found growing in fresh water environments) are often substituted for whole,
green terrestrial plants. Outline the advantages of this choice to
13
the experimenter. [6]
[Total: 16]
3 a Outline how the essential products of the light dependent stage of
photosynthesis are formed by non-cyclic photophosphorylation from
water, light energy, ADP and phosphate, and NADP. [10]
b Describe the steps of the Calvin cycle, establishing how the products of the

light-dependent stage are used, and identifying the products formed. [10]
[Total: 20]
4 a The enzyme rubisco is the most abundant, naturally occurring protein.
Where does rubisco occur, and what reaction does it catalyse? Suggest
why its abundance is to be expected. [4]
b By reference to rubisco, explain the principle of competitive inhibition
of an enzyme. [4]
c The reactions of photorespiration reduce the yield of photosynthesis.
Why is this so? [4]
[Total: 12]
5 a Fig. 5.1 is a diagram of part of a mitochondrion showing some of the
events occurring in oxidative phosphorylation.
inner intermembrane outer

matrix membrane space membrane
reduced H+ H+ H+
NAD H+
e– H+
NAD
H+
H+
H+
e–
H+
H+
H+
H+ H+
e– H+
H+
H+
H+
H+
e–
H+
H+
e– H+
Y
Z H+
H+ H+
H+
water
Key
= carrier
= movement of e –
= movement of H +
▲ Fig. 5.1
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i State two sources of the reduced NAD in Fig. 5.1. [2]
ii With reference to Fig. 5.1, outline the role of carriers in the inner
13 membrane. [2]
iii With reference to Fig. 5.1, name Y and Z. [2]
b Explain why it is an advantage to the cell for the inner membrane of the
mitochondrion to be folded. [2]
[Total: 8]
6 a S
how how both the absorption spectrum and the action spectrum of a
particular species of fresh water algae may be measured simultaneously.
13 Photosynthesis
b Draw and fully label the absorption and action spectra you would expect to be
produced, using a single graph.
c Describe in outline the steps by which the chlorophyll present in a sample of
green leaves can be obtained and the component pigments separated by means
of paper chromatography.
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A LEVEL
14 Homeostasis
14.1 Homeostasis in mammals

Cells function most Learning outcomes
efficiently if they are
kept in near constant
conditions. Cells in 14.1.1 explain what is meant by homeostasis and the importance of homeostasis
multicellular animals are in mammals
surrounded by tissue fluid. 14.1.2 explain the principles of homeostasis in terms of internal and external
The composition of tissue stimuli, receptors, coordination systems (nervous system and endocrine
fluid is kept constant by system), effectors (muscles and glands) and negative feedback
exchanges with the blood
14.1.9 describe the principles of cell signalling using the example of the control
as discussed in the topic
on Transport in mammals
of blood glucose concentration by glucagon, limited to: binding of hormone
(Topic 8). In mammals, to cell surface receptor causing conformational change; activation of
core temperature, blood G-protein leading to stimulation of adenylyl cyclase; formation of the
glucose concentration second messenger, cyclic AMP (cAMP); activation of protein kinase A
and blood water potential by cAMP leading to initiation of an enzyme cascade; amplification of the
are maintained within signal through the enzyme cascade as a result of activation of more and
narrow limits to ensure more enzymes by phosphorylation; cellular response in which the final
the efficient operation enzyme in the pathway is activated, catalysing the breakdown of glycogen
of cells. Prior knowledge
14.1.10 explain how negative feedback control mechanisms regulate blood
for this topic includes an
glucose concentration, with reference to the effects of insulin on muscle
understanding that waste
products are excreted from cells and liver cells and the effect of glucagon on liver cells
the body and an outline 14.1.11 explain the principles of operation of test strips and biosensors for
of the structure and measuring the concentration of glucose in blood and urine, with reference
function of the nervous to glucose oxidase and peroxidase enzymes
and endocrine systems.
In plants, guard cells
respond to fluctuations in Starting point
environmental conditions
and open and close ★ Homeostasis in mammals requires complex systems to maintain internal
stomata as appropriate conditions near constant.
for photosynthesis and
conserving water.
Maintaining a constant internal environment – homeostasis
Living things face changing and sometimes hostile environments. Some external
conditions change slowly, others dramatically. For example, temperature changes
quickly on land exposed to direct sunlight, but the temperature of water exposed to
sunlight changes very slowly.
How do organisms respond to environmental changes?
Some animals are able to maintain their internal environment, keeping it more or
less constant, allowing them to continue normal activities, at least over quite a wide
range of external conditions. These are the regulators. For example, mammals and
birds maintain a high and almost constant body temperature. Their bodies are kept
at or about the optimum temperature for the majority of the enzymes that drive their
metabolism. Their muscles contract efficiently and the nervous system co-ordinates
responses precisely, even when external conditions are unfavourable.
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Regulators are often able to avoid danger and they may also benefit from the
vulnerability of prey organisms which happen to be non-regulators. So regulators
14 may have greater freedom in choosing where to live. They can exploit more habitats
with differing conditions than ‘non-regulators’ can, too. But whether an organism is a
‘regulator’ or not, some of control of the internal environment is essential.
Homeostasis is the name we give to the ability to maintain a constant internal
environment. Homeostasis means ‘staying the same’. Mammals are excellent examples
of animals that keep their internal conditions remarkably constant (Figure 14.1). Their
internal environment is the blood circulating in the body and the fluid circulating
14 Homeostasis
among cells (tissue fluid) that forms from the blood plasma, delivering nutrients and
removing waste products while bathing the cells. Mammals successfully regulate
and maintain the pH, the concentrations of oxygen, carbon dioxide and glucose, the
temperature and the water content of their blood. All these are maintained at constant
levels or within very narrow limits.
How is homeostasis brought about and maintained?
polar bear on ice whale in the sea
otter in fresh water
camels in the desert

body
temperature
concentration of
respiratory gases in glucose level
blood (pCO2, pO2) of blood
mammals
pressure of examples of
water content
blood in homeostasis
of blood
arteries by negative
feedback
bat in the air
heart rate concentration of

essential ions
pH of blood
Mammals are a comparitively recent group in terms of

their evolutionary history, yet they have successfully
settled in significant numbers in virtually every type
of habitat on Earth. This success is directly linked to
their ability to control their internal environment by
homeostasis.
▲ Figure 14.1 Homeostasis in mammals
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components of a negative feedback control system
14
input – receptor coordinator effector output –
change to measures level level of operation is set here, and brings about a second condition restored
the system of the variable information from receptor received and change to system to set value
compared with set value, and commands (in opposite direction
to effector despatched from here to the input)
feedback loop
establishes the change has been corrected,

and causes the effector to be switched off

the laboratory water bath unit, an example
of a self-regulating system
coordinator with
on/off switch, pattern of change to water bath temperature
and set-point (water bath control set at 25°C)
scale
30
temperature temperature/°C 25
sensor
20 even with a highly efficient
receptor device it is
15 impossible to avoid some
heater/water ‘overshoot’ in regulation
stirrer 10
0 10 20 30
water temperature time/min
at start
▲ Figure 14.2 Negative feedback: the mechanism
Negative feedback – the mechanism of homeostasis

Negative feedback is a type of control in which the conditions being regulated are
brought back to a set value as soon as it is detected that they have deviated from it
(Figure 14.2). We see this type of mechanism at work in a laboratory water bath.
Analysis of this familiar example will show us the components of a negative feedback
system.
Question
A negative feedback system requires a receptor device that measures the value of
1 Homeostasis is the variable (in this case, the water temperature of the water bath) and transmits
illustrated in the way this information to a coordinator (in this case, the control unit). The coordinator
our bodies regulate compares data from the receptor with a pre-set value (the desired water temperature
carbon dioxide level. of the water bath). When the value is below the required value the coordinator
a Why is it essential switches on an effector device (a water heater in the water bath) so that the
that carbon temperature starts to increase. Once the water reaches the required temperature, data
dioxide in the from the receptor to this effect is received in the coordinator, which then switches off
blood does not the response (the water heater). How precisely the variable is maintained depends on
exceed a certain the sensitivity of the receptor, but negative feedback control typically involves some
level? degree of ‘overshoot’.
b In this example In mammals, regulation of body temperature, blood sugar level and the concentration
of homeostasis, of water and ions in blood and tissue fluid (osmoregulation) are all regulated by
identify where
negative feedback. The receptors are specialised cells either in the brain or in other
the receptor,
organs, such as the pancreas. The effectors are organs such as the skin, liver and
coordinator and
kidneys. Information passes between them either by impulses in neurones within
effectors occur in
our bodies. nerves of the nervous system or by hormones released into the blood by endocrine
organs. The outcome is an incredibly precisely regulated internal environment.
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The roles of the endocrine and nervous systems compared
14 The endocrine system and the nervous system work in distinctive and different ways
in the control and co-ordination of body activities. However, many of the activities of
the nervous and endocrine systems are coordinated by the pituitary gland, the master
gland of the endocrine system, working in tandem with the hypothalamus of the brain.
The hypothalamus secretes hormones that regulate the functioning of the pituitary. The
hypothalamus also monitors the level of hormones in the blood and regulates secretion
by negative feedback control.
14 Homeostasis
Endocrine system Nervous system

Communication by chemical messengers Communication by electrochemical action
transmitted in the bloodstream potentials (impulses) transmitted via neurones
Hormones ‘broadcast’ all over the body Action potentials are targeted on specific cells
but influence target cells and tissues only
Causes changes in metabolic activity Causes muscles to contract or glands to secrete
Have their effects over many minutes, Produces effects within milliseconds
several hours or longer
Effects tend to be long lasting Effects tend to be short lived and reversible
▲ Table 14.1 The endocrine and nervous systems compared
Homeostasis in action – control of blood glucose

concentration
Respiration is a continuous process in all living cells, and glucose is the principle
respiratory substrate for most tissues. To maintain tissue respiration, cells need a
regular supply of glucose. Transport of glucose to all cells is a key function of the
blood circulation. Fortunately, blood glucose can be quickly absorbed across the cell
membrane. In humans, the normal level of blood glucose is about 4 mM/L of blood,
but it varies, typically between 3.6 and 5.8 mM/L. The lower values arise during an
extended period without food, or after prolonged and heavy physical activity; the
highest values occur after a meal rich in carbohydrate has been digested.
Most cells (including muscle cells) hold reserves in the form of glycogen. This
polysaccharide is quickly converted to glucose during prolonged physical activity.
However, glycogen reserves may be used up quickly. (In the brain, glucose is the only
substrate the cells can use and there are no glycogen stores held in reserve there at all.)
The maintenance of a constant level of this monosaccharide in the blood plasma is the
norm, but two extreme conditions can arise:
» Hypoglycaemia, in which our blood glucose falls below 2.0 mM/L. If this is not
quickly reversed, we may faint. If the body, and particularly the brain, continue to be
deprived of adequate glucose levels, convulsions and coma follow.
» Hyperglycemia, in which an abnormally high concentration of blood glucose occurs.
Since a high concentration of any soluble metabolite lowers the water potential of the
blood plasma, water is drawn immediately from the cells and tissue fluid by osmosis,
back into the blood. As the volume of blood increases, water is excreted by the
kidney to maintain the correct concentration of blood. As a result, the body tends to
become dehydrated and the circulatory system is deprived of fluid. Ultimately, blood
pressure cannot be maintained.
For these reasons, it is critically important that the blood glucose is held within set limits.
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Regulation of blood glucose
Regulation of blood glucose is the result of the actions of two hormones, released from
groups of special cells, found in the pancreas. 14
After the digestion of carbohydrates in the gut, glucose is absorbed across the epithelium
cells of the villi (finger-like extensions of the inner surface of the small intestine) into the
hepatic portal vein. The blood carrying the glucose reaches the liver first. If the glucose
level is too high, then glucose starts to be withdrawn from the blood and is stored as
glycogen. However, not all of the glucose can be removed immediately. Blood circulating
in the body immediately after a meal has a raised level of glucose (Figure 14.3).

blood glucose serum insulin
mmol/litre pmol/litre
8.0 400
blood glucose levels

7.5
blood insulin levels 350
7.0 starch-rich food
sucrose-rich food 300
6.5
250
6.0
5.5 200
5.0
150
4.5
100
4.0
50
3.5
3.0 0
7a.m. 9a.m. 11a.m. 1p.m. 3p.m. 5p.m. 7p.m. 9p.m. 11p.m. 1a.m. 3a.m. 5a.m. 7a.m.
breakfast lunch dinner
▲ Figure 14.3 How blood glucose and insulin levels vary with time
At the pancreas, the presence of an excess of blood glucose is detected in patches of

cells known as the islets of Langerhans. These islets are hormone-secreting glands
(endocrine glands); they have a rich capillary network, but no ducts that would carry
secretions away. Instead, they are transported all over the body by the blood. The islets
of Langerhans contain two types of cell, alpha (α) cells and beta (β) cells (Figure 14.4).
TS of pancreatic gland showing an islet of Langerhans drawing of part of pancreatic gland

duct carries pancreatic cells of pancreatic
juice to duodenum gland surrounding islet
of Langerhans secrete
pancreatic juice
islet of
α cells
Langerhans
β cells
blood capillary
▲ Figure 14.4 An islet of Langerhans in the pancreas
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Question 2 Given the role of alpha cells and beta cells (the production and discharge of hormones),
14 identify the organelles that are involved directly and list their specific roles.
In the presence of a raised blood glucose level, the beta cells are stimulated. They
secrete the hormone insulin into the capillary network. Insulin stimulates the uptake
of glucose by cells all over the body, but especially by the liver and the skeletal muscle
fibres. Another effect of insulin is to trigger the conversion of glucose to glycogen
(glycogenesis) and of glucose to fatty acids and fats in liver cells. Insulin also promotes
the deposition of fat around the body (Figure 14.5).
14 Homeostasis
As the blood glucose level reverts to normal this is detected in the islets of Langerhans,
and the beta cells respond by stopping insulin secretion. Meanwhile the hormone is
excreted by the kidney tubules and the blood insulin level falls (Figure 14.6).
When the blood glucose level falls below normal, the alpha cells are stimulated.
These secrete a hormone called glucagon. This hormone activates the enzymes that
convert glycogen and amino acids to glucose (gluconeogenesis). Glucagon also reduces
the rate of respiration.
As the blood glucose level reverts to normal, glucagon production ceases, and this
hormone in turn is removed from the blood in the kidney tubules.
liver
imports glucose when blood
small intestine glucose level is high; exports glucose
glucose absorption amino acid when blood glucose level is low
glucose
NH2
NH2
glucose glycogen
brain cells fat

import glucose as required the blood circulation connects
all organs (directly or indirectly) pancreas
(but do not store glycogen)
contains special cells of two
types (in the islets of
α Langerhans) that are sensitive
glucose glucose to the level of sugar in the blood
β
α cells secrete glucagon
glucose when glucose level is low
glycogen β cells secrete insulin
when glucose level is high
most tissues glucagon causes
glycogen muscles
can import or export glucose insulin causes lowering raising of blood
can import glucose
but do not export it of blood glucose level glucose level
▲ Figure 14.5 Distribution and metabolism of blood glucose
Figure 14.6 Glucose

glucagon
regulation by negative secreted glucagon secretion
feedback detected in islets of by α cells in liver glycogen and amino acids stops (negative
Langerhans of pancreas are converted into glucose feedback) – glucagon
excreted by the
kidneys
fall in blood glucose
(starvation, physical activity) rise in blood glucose
normal glucose level of the normal blood

blood (about 4 mmol/litre) glucose level
fall in blood glucose

rise in blood glucose
liver:
(after meal)
glucose glycogen, insulin secretion
cell respiration increased, stops (negative
detected in islets of glucose fatty acids + fats feedback) – insulin
Langerhans of pancreas excreted by the
muscle:
glucose glycogen, kidneys
insulin secreted by β cells cell respiration increased
other tissues:
cell respiration increased
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The role of cyclic AMP in the effects of glucagon on liver cells
Glucagon is a peptide hormone, which, while circulating in the bloodstream, stimulates
liver cells to convert stored glycogen to glucose. The glucose formed then passes out 14
from the liver cells and contributes to blood glucose levels.
The actions triggered by glucagon are brought about within the liver cells without the
hormone having passed through the cell’s cell surface membrane. Instead, the hormone
binds to specific receptors in the cell surface membrane, and this event triggers the
following changes:
» First, another membrane-embedded protein, known as a G-protein, is activated.

» The activated G-protein in turn activates an enzyme known as adenylyl cyclase, also
embedded in the cell surface membrane.
» Activated adenylyl cyclase catalyses the formation of cyclic AMP (cAMP) from ATP
within the cell cytosol (Figure 14.7).
cAMP is known as a second messenger. It is a small, non-protein molecule that is water
soluble, and so spreads quickly through the cytosol by diffusion. The presence of this
second messenger triggers a cascade of reactions in liver cells in which specific enzymes
are activated by reaction with ATP. The outcomes are:
» the hormone signal is amplified
» the glycogen stored in the liver cells is hydrolysed to glucose.
These events are summarised in Figure 14.7.
blood supply
to liver glucagon
glucagon glucagon does receptor

not enter cell
binds to receptor cell surface
in cell surface membrane G-protein membrane
ATP cyclic AMP adenylyl

cyclase
existing
(inactive) cAMP eventually
protein activated inactivated
enzyme
ATP
cyclic AMP (cAMP)
structure/ second messenger
function
of cell
altered
activated enzyme
system in liver cell
liver cell
glycogen glucose
▲ Figure 14.7 The role of cyclic AMP as a second messenger
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The three-stage process of cell-signalling
14 The impact of glucagon on a liver cell is a three-stage process of cell signalling

(Figure 14.8). After the first stage, when a hormone molecule interacts at the cell surface,
subsequent events are activated by a succession of relay molecules, initiated by the
formation of a second messenger, cAMP, within the cytosol.
cAMP
inactive kinase enzyme
active kinase enzyme

14 Homeostasis
inactive phosphorylase enzyme
active phosphorylase enzyme
glycogen
glucose 1-phosphate
▲ Figure 14.8 The three stages of cell-signalling
The relay molecules are activated kinases and phosphorylases. These proteins catalyse
specific types of reaction:
» Kinases are enzymes that transfer a phosphate group from ATP to an acceptor.
» Phosphorylases are enzymes that break down glucose-based polysaccharides (e.g.
glycogen) to glucose 1-phosphate.
The critical role of the second and third stages of signal transduction is the amplification
of the hormone signal. So, from one activated receptor molecule, 10 000 (104) molecules
of cAMP are formed. As a result of the presence of cAMP in the cytosol, approximately
106 molecules of active phosphorylase enzyme will be formed, and these will then trigger
the formation of perhaps 108 molecules of glucose 1-phosphate.
Stage Events Consequences

1 hormone interaction at the cell surface a single hormone initiates events
2 formation of cyclic AMP, which binds about 104 molecules of cAMP become
to kinase proteins active in the cytosol
ATP → cAMP
3 an enzyme cascade involving approximately 108 molecules of glucose
activation of enzymes by 1-phosphate are formed and become
phosphorylation to amplify the signal available to pass out into the bloodstream
▲ Table 14.2 Stages of signal transduction leading to amplification
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EXTENSION
The disease of diabetes
14
Diabetes is the name for a group of diseases in which the body fails to regulate blood glucose levels. Type I
diabetes results from a failure of insulin production by the beta cells. It is also referred to as insulin-dependent
diabetes, early onset diabetes or juvenile diabetes (because it typically appears early on in a person’s life). Type
II diabetes is a failure of the insulin receptor proteins on the cell surface membranes of target cells. It is also
referred to as diabetes mellitus, late onset diabetes or adult onset diabetes.

As a consequence of either form of the disease, blood glucose regulation is more erratic and, generally, the level
of glucose is permanently raised – to dangerous levels in untreated cases of Type I diabetes. Glucose is also
regularly excreted in the urine. If this condition is not diagnosed and treated, it carries a risk of circulatory
disorders, renal failure, blindness, strokes and heart attacks.
The production of human insulin for treatment of diabetes by the genetic engineering of bacteria is discussed in
Topic 19.
Type I diabetes (insulin-dependent Type II diabetes (diabetes mellitus, late onset
diabetes, early onset diabetes or juvenile diabetes or adult onset diabetes):
diabetes): » The common form (90% of all cases of
» Affects young people, below the age of diabetes are of this type)
20 years due to the destruction of the » Common in people over 40 years especially
β cells of the islets of Langerhans by the if overweight, but this form of diabetes
body’s own immune system is having an increasing effect on human
» Symptoms: societies around the world, including on
– constant thirst young people and even children in developed
– undiminished hunger countries, seemingly because of poor diet
– excessive urination » Symptoms:
» Treatment: – mild sufferers usually have sufficient
– injection of insulin into the blood blood insulin, but insulin receptors on
stream daily cells have become defective
– regular measurement of blood » Treatment:
glucose level – largely by diet alone
Dip-sticks and biosensors for quantitative measurements

of glucose
Dip sticks, such as Clinistix™ or, alternatively biosensors, are used to measure glucose
levels in urine or blood.
Glucose is not present in the urine of a healthy person because, although it appears
in the filtrate in the Bowman’s capsule of the kidney, it is selectively reabsorbed in the
proximal convoluted tubules (page 305). However, people with diabetes cannot control
their blood sugar levels effectively. Glucose may appear in the urine when the blood
sugar levels rise steeply, for example after a meal. Diabetics may need to inject insulin to
reduce blood sugar levels. The urine may be tested to find out if an injection is needed
using Clinistix™ (see Figure 14.9, overleaf). Alternatively, a glucose biosensor may be
used (see Figure 14.10, overleaf).
The Clinistix™ strip contains two enzymes, glucose oxidase and peroxidase, together with
a colourless hydrogen donor compound called chromogen. When the strip is dipped into the
urine sample, if glucose is present it is oxidised to gluconic acid and hydrogen peroxide. The
second enzyme catalyses the reduction of hydrogen peroxide and the oxidation of chromogen.
The product is water and the oxidised dye, which is coloured. The more glucose present in the
urine, the more coloured dye is formed. The colour of the test strip is then compared to the
printed scale to indicate the amount of glucose in the urine (Figure 14.9).
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the principles
glucose oxidase
14 glucose + oxygen gluconic acid + H2O2
peroxidase
DH2 + H2O2 2H2O + D
reduced chromagen
chromagen (coloured)
(colourless)
14 Homeostasis
the process
test strip dipped

into urine sample
▲ Figure 14.9 Measuring glucose in urine using a Clinistix™
An alternative approach for the person with diabetes is to measure the glucose level
in the blood itself using a glucose biosensor (Figure 14.10). A biosensor is a device
which makes use of a biological molecule (or sometimes a cell) to detect and measure a
chemical compound.
tip of probe
‘unpacked’
and enlarged
platinum
electrode
cellulose
acetate
layer
immobilised
enzyme
layer
polycarbonate
layer
blood
contact
▲ Figure 14.10 Biosensor for blood glucose testing
Question
The glucose biosensor has an immobilised enzyme, glucose oxidase, held between two
3 What are the membranes positioned at the tip of a platinum electrode. In use, the outer membrane
advantages to a is momentarily brought in contact with a tiny drop of blood, squeezed from a pinprick
diabetic patient of puncture of the skin at the tip of a finger. In contact with the immobilised enzyme,
measuring blood glucose in the blood plasma is immediately oxidised to gluconic acid and hydrogen
glucose by means peroxide. The electrode measures the drop in oxygen used to produce the hydrogen
of a biosensor, peroxide and an electrical signal is generated. The size of this signal is proportional
compared to the to the concentration of glucose in the patient’s blood. A digital read-out gives the
Clinistix™ method? concentration of blood glucose.
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14.1 continued…Kidneys – structure and function
14
Learning outcomes
14.1.3 state that urea is produced in the liver from the deamination of excess
amino acids
14.1.4 describe the structure of the human kidney, limited to: fibrous capsule,
cortex, medulla, renal pelvis, ureter, branches of the renal artery and

renal vein
14.1.5 identify, in diagrams, photomicrographs and electron micrographs,
the parts of a nephron and its associated blood vessels and structures,
limited to: glomerulus, Bowman’s capsule, proximal convoluted tubule,
loop of Henle, distal convoluted tubule, collecting duct
14.1.6 describe and explain the formation of urine in the nephron, limited to:
the formation of glomerular filtrate by ultrafiltration in the Bowman’s
capsule, selective reabsorption in the proximal convoluted tubule
14.1.7 relate the detailed structure of the Bowman’s capsule and proximal
convoluted tubule to their functions in the formation of urine
14.1.8 describe the roles of the hypothalamus, posterior pituitary gland,
antidiuretic hormone (ADH), aquaporins and collecting ducts in
osmoregulation
Starting points
★ The kidneys remove wastes from the blood and are the effectors for
controlling the water potential of the blood.
Excretion, blood water balance and metabolic waste

Excretion is a characteristic activity of all living things. It is essential because the
chemical reactions of metabolism produce byproducts, some of which would be toxic if
allowed to accumulate. Excretion is the removal from the body of the waste compounds
produced during the metabolism of cells.
Humans excrete carbon dioxide from the lungs
Biochemical change Fate of products and urea in urine produced by our kidneys.
In mammals, excretion is a part of the process
1. proteins digested to amino acids
of homeostasis. Excretion of nitrogenous
2. Excess amino acids are then deaminated: compounds is important in animals because
OH2 metabolised to pyruvate respired via the they do not store protein. Proteins in the
Krebs cycle diet are broken down to their constituent
2CH3 CH amino acids. Amino acids that are excess to
amino acid requirements for protein synthesis are respired.
e.g. alanine NH2 2NH3
The first step is called deamination. This
occurs in the liver and is the removal from
3. Formation of urea: each amino acid of its amino group, which
becomes ammonia. Ammonia is a very soluble
NH2
and extremely toxic compound. However, the
2NH3 + CO2 C O + H 2O excreted by the ammonia is promptly converted into a safer
kidneys nitrogenous compound. In mammals that
NH2 compound is urea – formed by reaction of
ammonia with carbon dioxide (Figure 14.11).
▲ Figure 14.11 Deamination In dilute solution, urea is safely excreted from
the body.
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Associated with excretion, and very much part of it, is the process of osmoregulation.
Osmoregulation is the maintenance of a proper balance in the water and dissolved
14 substances in the blood. Excretion and osmoregulation together, are the work of our kidneys.
The kidney – an organ of excretion and osmoregulation

The role of our kidneys is to regulate the internal environment is by constantly
adjusting the composition of the blood. Waste products of metabolism are transported
from the metabolising cells by the blood circulation, removed from the blood in the
kidneys and excreted in a solution called urine. At the same time, the concentrations
of inorganic ions, such as sodium (Na+) and chloride (Cl–) ions, and water in the body
14 Homeostasis
are also regulated.

The position of the kidneys is shown in Figure 14.12. Each kidney is served by a renal
artery and drained by a renal vein. Urine from the kidney is carried to the bladder
by the ureter and from the bladder to the exterior by the urethra, when the bladder
sphincter muscle is relaxed. Together these structures are known as the urinary system.
thorax
diaphragm
kidney
(attached to
dorsal wall)
renal vein
renal artery
ureter
vena cava dorsal aorta
sphincter
muscle –
under bladder
voluntary
control urethra
▲ Figure 14.12 The human urinary system
In section, each kidney consists of an outer cortex and inner medulla, and these
are made up of a million or more nephrons. A nephron is thin-walled tubule about
3 cm long, part in the cortex and part in the medulla. The shape of a nephron and its
arrangement in the kidney are shown in Figure 14.13.
Blood vessels are closely associated with each of the distinctly-shaped regions of the
nephrons. For example, the first part of the nephron is formed into a cup-shaped
Bowman’s capsule and the capillary network here is known as the glomerulus.
Collectively, these are known as the Malpighian body. They occur in the cortex.
The convoluted tubules occur partly in the cortex and partly in the medulla, but
notice that the extended loops of Henle and collecting ducts largely occur in the
medulla.
Each region of the nephron has a specific role to play in the work of the kidney, and the
capillary network serving the nephron plays a key part, too, as we shall now see.
The formation of urine

In humans, about 1–1.5 litres of urine are formed each day, typically containing
about 40–50 g of solutes, of which urea (about 30 g) and sodium chloride (up to 15 g)
make up the bulk. The nephron produces urine in a continuous process which we
can conveniently divide into five steps, to show just how the blood composition is so
precisely regulated.
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LS through kidney showing positions of nephrons in cortex nephron with blood capillaries
and medulla
14
Bowman’s
1 Malpighian body capsule
glomerulus
fibrous capsule
nephrons 2 proximal convoluted
tubule
collecting duct 4 distal convoluted
tubule
renal artery

renal pelvis – cortex
expanded
branch of capillary medulla
origin of
ureter renal artery network to
convoluted
branch of tubules
medulla renal vein
ureter
cortex
3 loop of Henle
descending limb
Roles of the parts of the nephron ascending limb
1 Malpighian body = ultrafiltration
2 proximal convoluted tubule = selective
vasa recta 5 collecting duct
reabsorption from filtrate
3 loop of Henle = water conservation (capillary to
4 distal convoluted tubule = pH adjustment loop of Henle)
and ion reabsorption
5 collecting duct = water reabsorption
Photomicrograph of the cortex of the kidney in section, showing the tubules, Bowman’s capsules and capillary networks
distal
Bowman’s and
capsule proximal
convoluted
glomerula tubules
capillaries in section
containing
red cells
▲ Figure 14.13 The kidney and its nephrons: structure and roles
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Question Step 1: Ultrafiltration in the Bowman’s capsule
14 4 a W
hat is the
source of the
In the glomerulus, water and relatively small molecules of the blood plasma, including
useful ions, glucose and amino acids pass out of the capillaries, along with urea, into the
force that drives lumen of the capsule. This process is described as ultrafiltration because it is powered
ultrafiltration in by the pressure of the blood. The blood pressure is raised at this point by the input
the glomerulus? capillary (afferent arteriole) being wider than the output capillary (efferent arteriole).
This increase in hydrostatic (blood) pressure exceeds the water potential of the plasma.
b List the main
This forces water and the soluble components of plasma that are able to pass out
components of
through the extremely fine sieve-like wall structure here, between the podocytes, into
the blood that
14 Homeostasis
are likely to be the capsule. This sieve is made of two layers of cells (the endothelium of the capillaries
filtered in the of the glomerulus and the epithelium of the capsule), between which is a basement
nephron. membrane. You can see this arrangement in Figure 14.14.
afferent arteriole efferent arteriole

(wide) foot-like extensions of podocytes
(narrow)
wrap around capillary
capillaries of
the glomerulus capillary wall basement
with pores water and membrane pores in
(high blood
other small (the final capillary
pressure here) basement
molecules filter) wall
membrane
wall of pass out
Bowman’s
capsule
(squamous nucleus of
epithelium) podocyte
podocytes blood under cell
path of filtrate into pressure (cells
lumen of nephron and plasma path of filtrate from capillary to
cells of proximal proteins lumen of the Bowman’s capsule
convoluted tubule retained here) between (not through) the podocytes
False-colour SEM of podocytes (pale purple) with their extensions wrapped around the
blood capillaries (pink/red) (×3500)
podocytes
with their
extensions
wrapped around
blood capillaries
▲ Figure 14.14 The site of ultrafiltration
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Notice that the cells of the capsule wall are called podocytes for they have feet-
Question
like extensions that form a network with tiny slits between them. Similarly, the
5 a C
ells of the walls
of the proximal
endothelium of the capillaries has pores, too. This detail was discovered using the
electron microscope, because these filtration gaps are very small indeed. So small,
14
convoluted in fact, that not only are blood cells retained, but the majority of blood proteins and
tubule have a polypeptides dissolved in the plasma also remain in the circulating blood. It is the
brush border presence of the basement membrane that stops large proteins passing out. So, the
(Figure 14.16). fluid that has been filtered through into the Bowman’s capsule is very similar
Explain why this to blood plasma but with the significant difference that protein molecules are
feature is helpful largely absent.

to the process of
reabsorption.
Step 2: Selective reabsorption in the proximal convoluted tubule
b What does
The proximal convoluted tubule is the longest section of the nephron and it is here that a
facilitated
diffusion involve? large part of the filtrate is reabsorbed into the capillary network. The walls of the tubule
are one cell thick and their cells are packed with mitochondria.
cell surface
The electrochemical gradient in H+ ions
membrane
between the exterior and the interior of inside outside
the cell drives the active transport of the cell the cell
metabolites (e.g. sugars, amino acids) (filtrate)
across the membrane as the H+ flow high concentration of H+
down their electrochemical gradient via ATP (store of potential energy)
the cotransporter pump. ADP + Pi built up outside the cell
surface membrane by the
proton pump
proton pump driven by
energy transferred from ATP
H+ ions
molecules
▲ Figure 14.15 Cotransport: of sugar
active transport driven by
a concentration gradient cotransporter
pump
harmful substances
capillary water movement
actively transported
wall cells by osmosis
from blood into filtrate
filtrate flow
in lumen
proximal
convoluted
tubule wall cell glucose + amino ions (e.g. Na+) by the few proteins
reabsorbed acids actively • active transport in filtrate are taken
transported • facilitated diffusion back into blood
across membranes • exchange with H+ ions by pinocytosis
▲ Figure 14.16 Reabsorption in the proximal convoluted tubule
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(We would expect this, if active transport is part of the way reabsorption is brought
about.) The cell surface membranes of the cells of the tubule wall in contact with the
14 filtrate all have a ‘brush border’ of microvilli. These microvilli increase enormously the
surface area where reabsorption occurs. The mechanisms of reabsorption are:
» active transport of sugars and amino acids across the cell surface membrane by the
activity of special carrier proteins in a process known as cotransport (Figure 14.15).
In this, the carrier protein uses the diffusion of hydrogen ions (protons) down their
electrochemical gradient into the cell to drive the uptake of molecules of sugars such
as glucose or sucrose, typically against their concentration gradient. Other essential
metabolites are transported similarly.
14 Homeostasis
» movement of mineral ions by a combination of active transport, facilitated

diffusion and some exchange of ions
» diffusion of urea
» movement of proteins by pinocytosis
» some movement of water by osmosis.
Step 3: Water conservation in the loop of Henle

The function of the loop of Henle is to enable the kidneys to conserve water. Since urea
is expelled from the body in solution, some water loss during excretion is inevitable.
There is a potential problem here. Water is a major component of the body and it is often
a scarce resource for terrestrial organisms. It is important, therefore, that mammals
are able to form urine that is more concentrated than the blood (when necessary),
thereby reducing the water loss to a minimum. Human urine can be up to five times as
concentrated as the blood.
The structure of the loop of Henle with its descending and ascending limbs,
together with a parallel blood supply, the vasa recta, is shown in Figure 14.17.
The vasa recta is part of the same capillary network that surrounds a nephron.
loop of Henie
vasa recta descending limb direction of blood flow
ascending limb in the vasa recta
direction of filtrate flow
in the ascending limb
direction of filtrate flow
in the descending limb
here the walls are

–
H2O permeable to ions (Na,+ Cl ),
but impermeable to water
Na+ Na+ –
here the walls are – Cl
– Na+ and Cl are actively
Cl
permeable to ions and transported out
H2O
water
tissue of medulla
H 2O
the rising concentration
H 2O
of ions outside causes there is a gradient in
loss of water by concentration of ions
osmosis across the medulla
Na+
the vasa recta –
delivers oxygen to Cl
H2O
the cells of the –
tubule walls Na+ and Cl diffuse out from
this concentrated solution
H 2O
water loss causes the

A high concentration of salts is formed in the medulla, solution of ions to
which allows water to be absorbed from the nearby become concentrated
collecting ducts. here
▲ Figure 14.17 The functioning of the loop of Henle
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The role of the loops of Henle and their capillary loops is to create and maintain an
osmotic gradient in the medulla of the kidney. The gradient across the medulla is
from a less concentrated salt solution near the cortex to the most concentrated salt
solution at the tips of the pyramid region of the medulla. The pyramid region of the
14
medulla consists mostly of the collecting ducts. The osmotic gradient allows water
to be withdrawn from the collecting ducts if circumstances require it. How this is
occurs we shall discuss shortly. First, there is the question of how the gradient itself
is created by the loops of Henle.
The gradient is brought about by a mechanism known as a counter-current

multiplier. The principles of counter-current exchange here involve exchange
between fluids flowing in opposite directions in two systems. The annotations in
Figure 14.17 help show how the counter-current mechanism works. In following
these annotations, remember that the descending and ascending limbs lie close
together in the kidney.
Look first at the second half of the loop, the ascending limb. The energy to create the
gradient is transferred from ATP to drive ion pumps in the wall cells of the ascending
limbs. Here, sodium and chloride ions are pumped out of the filtrate into the fluid
between the cells of the medulla, called the interstitial fluid. The walls of the ascending
limbs are unusual in being impermeable to water. So water in the ascending limb is
retained in the filtrate as salt is pumped out.
Opposite is the first half of the loop, the descending limb. This limb is fully permeable to water
and also to most salts. Here, water passes out into the interstitial fluid by osmosis, due to the
salt concentration in the medulla. At the same time and for the same reason, sodium, chloride
and other ions tend to pass in.
Exchange in this counter-current multiplier is a dynamic process occurring down
the whole length of the loop. At each level of the loops, the salt concentration in
the descending limb is slightly higher than the salt concentration in the adjacent
ascending limb. As the filtrate flows, the concentrating effect is multiplied and so the
fluid in and around the hairpin bend of the loops of Henle is the saltiest.
The role of the vasa recta is first to deliver oxygen to and remove carbon dioxide from
the metabolically active cells of the loop of Henle. As it does this, the blood in the vasa
recta also becomes saltier as it flows down beside the ascending limb and less salty as
it flows back up and out of the medulla. In this way the cells of the loop are serviced
without removing the accumulated salts from the medulla. The vasa recta does absorb
water that has passed into the medulla at the collecting ducts. We discuss the working
of these ducts in step 5 below.
Question 6 What is the essential feature of a counter-current flow system?
Step 4: Blood pH and ion concentration regulation in the distal

convoluted tubule
The cells of the walls of the distal convoluted tube are of the same structure as those of
the proximal convoluted tubule, but their roles differ somewhat.
Here the cells of the tubule walls adjust the composition of the blood, in particular, the
pH. Any slight tendency for the pH of the blood to change is initially prevented by the
blood proteins. Protein acts as a pH buffer.
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However, if the blood does begin to deviate from pH 7.4, then here in the distal
convoluted tubule there is a controlled secretion of hydrogen ions (H+) combined with
14 reabsorption of hydrogencarbonate ions (HCO3 –). Consequently, the pH of the blood
remains in the range pH 7.35–7.45, but the pH of urine can vary widely, in the range
pH 4.5–8.2.
Also in the distal convoluted tubule, the concentration of useful ions is regulated.
In particular, the concentrations of potassium ions (K+) is adjusted by secretion of any
excess present in the plasma into the filtrate. Similarly, the concentration of sodium ions
(Na+) in the body is regulated by varying the quantity of sodium ions reabsorbed from
14 Homeostasis
the filtrate.
Step 5: Water reabsorption in the collecting ducts

When the intake of water exceeds the body’s normal needs then the urine produced is
copious and dilute. We notice this after we have been drinking a lot of water. On the
other hand, when we have taken in very little water or when we have been sweating
heavily (part of our temperature regulation mechanism) or if we have eaten very salty
food perhaps, then a small volume of concentrated urine is formed.
Osmoregulation, the control of the water content of the blood (and therefore of the
whole body) is a part of homeostasis – another example of regulation by negative
feedback.
How exactly is this brought about?
The hypothalamus, part of the floor of the forebrain (Figure 14.18), controls many
body functions. The composition of the blood is continuously monitored here, as it
circulates through the capillary networks of the hypothalamus. Data is also received
at the hypothalamus from sensory receptors located in certain organs in the body.
All these inputs enable the hypothalamus to accurately control the activity of the
pituitary gland.
The pituitary gland is situated below the hypothalamus, but is connected to it
(Figure 14.18). The pituitary gland as a whole produces and releases hormones (it
is part of our endocrine system, see below) – in fact it has been called the master
hormone gland. In the process of osmoregulation, it is the posterior part of the
pituitary that stores and releases antidiuretic hormone (ADH) – among others.
(Other parts of the pituitary secrete hormones regulating a range of other body
activities and functions.)
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The hypothalamus and the cerebral hemispheres
pituitary gland
14
hypothalamus and
pituitary gland enlarged cerebellum
14.1 continued … Kidneys – structure and function

medulla
neurosecretory cells
hypothalamus
capillary
network
neurosecretory cells
portal vein artery

(begins and
ends as a
capillary)
anterior lobe lobe of

of pituitary pituitary
hormone
secreting cells
vein
vein artery
capillary
hormones to body cells network
A neurosecretory cell
of the hypothalamus
synapses with neurones of CNS
mitochondria neurosecretory hormone secreted
vesicles into blood stream
action potential
ADH
axon
cell body nerve ending
neurosecretory cell
basement capillary wall
membrane
capillary
▲ Figure 14.18 The hypothalamus and pituitary gland, and the release of ADH
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Antidiuretic hormone (ADH) is actually produced in the hypothalamus and stored in
vesicles at the ends of neurosecretory cells in the posterior pituitary gland. When nerve
14 impulses from the hypothalamus trigger the release of ADH into the capillary networks
in the posterior pituitary, ADH circulates in the bloodstream. However, the targets of
this hormone are the walls of the collecting ducts of the kidney tubules.
When the water content of the blood is low, antidiuretic hormone (ADH) is secreted
from the posterior pituitary gland. When the water content of the blood is high, little or
no ADH is secreted.
How does ADH change the permeability of the walls of the collecting ducts?
14 Homeostasis
The cell surface membranes of the cells that form the walls of the collecting ducts
contain a high proportion of channel proteins called aquaporins that are capable of
forming an open pore running down their centre. Some aquaporins, aquaporin-1,
are permanent in most membranes, but in the distal convoluted tubule additional
aquaporins, called aquaporin-2, can be opened in response to ADH. You can see the
structure of a fluid mosaic membrane and its channel proteins in Figure 4.3 (page 83)
and Figure 4.11 (page 90). Aquaporins are selectively permeable to water molecules
and therefore increase the rate of water diffusion (osmosis) through the membrane.
This is because the water molecules no longer have to pass through the lipoprotein
membrane structure that restricts their flow. In this way the presence of ADH ensures
that a maximum volume of water can be reabsorbed into the medulla of the kidney
and back into the bloodstream.
When ADH is present in the blood circulating past the kidney tubules, this hormone
causes the protein channels present in the collecting duct cell surface membranes to be
open. As a result, much water diffuses out into the medulla and very little diffuses from
the medulla into the collecting ducts (Figure 14.19).
Can you explain why? You may need to go back to step 3 above.
The water entering the medulla is taken up and redistributed in the body by the blood
circulation. Only small amounts of very concentrated urine are formed. Meanwhile, as
ADH circulates in the blood, the actions of the liver continually remove this hormone and
inactivate it. This means that the presence of freshly released ADH has a regulatory effect.
When ADH is absent from the blood circulating past the kidney tubules, the protein
channels in the collecting duct cell surface membranes are closed. The amount of
water that is retained by the medulla tissue is now minimal. The urine become
copious and dilute.
Questions 7 a L ist the components of a negative feedback system and identify these components
in the process of osmoregulation.
b How is the effect of ADH on the collecting ducts fed back to the coordinator?
8 Why is too much water rarely a problem for plant cells, but potentially hazardous to
animal cells?
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Water reabsorption in the collecting ducts
When we have: When we have:
• drunk a lot of water
the hypothalamus detects this and stops the
• taken in little water
• sweated excessively
14
posterior pituitary gland secreting ADH. • eaten salty food
the hypothalamus detects this and directs the
posterior pituitary gland to secrete ADH.
ADH absent ADH present

collecting duct walls less permeable collecting duct walls permeable
14.1 continued … Kidneys – structure and function

cortex
medulla
water stays in
the collecting
duct
water diffuses
into medulla
small quantity
a lot of dilute of concentrated
urine formed urine formed
high concentration high concentration
of solutes in medulla of solutes in medulla
Osmoregulation by negative feedback

osmoreceptors of pituitary
hypothalamus secretes collecting duct walls
not stimulated less ADH less permeable, so
+ medulla absorbs less
thirst receptors no feeling of thirst, water from the
not stimulated little water drunk collecting ducts
too much water

(or too little salts)
i.e. raised large volume
(becomes less negative) of dilute
urine formed
blood plasma at blood plasma at

normal concentration – ADH present in plasma normal concentration –
correct water potential ( ) is excreted in kidneys correct water potential ( )
small volume
too little water of concentrated
(or too much salt) urine formed
i.e. lowered
(becomes more negative)
collecting duct
thirst receptors feeling of thirst,
walls more
stimulated water likely to
permeable, so
+ be drunk
medulla absorbs more
osmoreceptors of
water from the
hypothalamus pituitary
collecting ducts
stimulated secretes more ADH
▲ Figure 14.19 The collecting ducts and their role in osmoregulation
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14.2 Homeostasis in plants
14.2.1 explain that stomata respond to changes in environmental conditions by
opening and closing and that regulation of stomatal aperture balances
the need for carbon dioxide uptake by diffusion with the need to minimise
water loss by transpiration
14.2.2 explain that stomata have daily rhythms of opening and closing
14 Homeostasis
14.2.3 describe the structure and function of guard cells and explain the
mechanism by which they open and close stomata
14.2.4 describe the role of abscisic acid in the closure of stomata during times of
water stress, including the role of calcium ions as a second messenger
Starting point
★ Stomatal aperture is regulated in response to the requirements for uptake of
carbon dioxide for photosynthesis and conserving water.
thick wall prevents The stomata – structure and role

movement in this plane
The tiny pores of the epidermis of leaves through which gas exchange
can occur are known as stomata. Most stomata occur in the leaves,
but some do occur in stems. In the broad-leaved plants, stomata are
typically concentrated in the lower epidermis of the leaves. In the
narrow, pointed leaves typical of many grasses for example, stomata
may be equally distributed on both surfaces. The structure of stomata
was introduced in Topic 7 (Figure 7.11 on page 153).
Remind yourself of their structure, now.
Each stoma consists of two elongated guard cells. These cells are
attached to ordinary epidermal cells that surround them and are
securely joined together at each end, but are detached and free to
pressure potential in the thin walls allow
guard cells causes a pore cell to bend in separate along their length, forming a pore between them. When
to open between this plane open, stomatal pores connect the atmosphere external to the
▲ Figure 14.20 The thickness of guard cell walls
leaf with the air spaces between the living cells of leaf and stem.
and opening/closing movements All these air spaces are interconnected. This is the pathway of
diffusion of carbon dioxide into the leaf, and of water vapour out.
the pattern of opening and closing of stomata
over 24 hours (as observed in potato leaf)
Stomata open and close due to changes in turgor pressure of the guard cells.
They open when water is absorbed by the guard cells from the surrounding
epidermal cells. The guard cells then become fully turgid and they push into
the epidermal cell besides them. This is because of the variable thickness of
cellulose in the walls, and because of the way cellulose fibres are laid down
11 1 2 there (Figure 14.20). A pore then develops between the guard cells. When
10
8
9 noon 3
4
water is lost and the guard cells become flaccid, the pore closes again. This
7 5 has been demonstrated experimentally (see Figure 14.22).
6 6
5 7 Stomata have a daily rhythm: they tend to open in daylight and close in the
4 8
3 9 dark (but there are exceptions to this diurnal pattern). This pattern of opening
2 10
1 mt 11 and closing of stomata, over a 24-hour period, is shown in Figure 14.21.
closed
opening This daily pattern is overridden, however, if and when the plant becomes
short of water and starts to wilt. For example, in very dry conditions when
there is an inadequate water supply, stomata inevitably close relatively early
▲ Figure 14.21 The diurnal pattern of
in the day (because turgor cannot be maintained). This closure curtails
stomatal opening and closing water vapour loss by transpiration and halts further wilting. Adequate water
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In an experimental demonstration that turgor Observation: on release of the turgor pressure
pressure of the guard cells causes the opening in one guard cell, the distinctive shape of the
of the stomatal pore, a microdissection needle
was inserted into a guard cell.
cell when the pore is open was lost. ‘Half’ of
the pore disappeared. 14
A fully open pore B microdissection needle (fine hollow tube) C half-open pore
due to turgid guard cells inserted into one guard cell vacuole due to collapse of turgor
cell sap (fluid)

needle pushed in
escapes

Before the experiment the After the experiment the pore
stomatal pore was fully open, was half-open, due to collapse
due to the turgor of the guard of turgor in one guard cell.
cells.
▲ Figure 14.22 The opening of stomata is a result of turgor pressure
reserves from the soil may be taken up subsequently, thereby allowing the opening of
stomata again, for example, on the following day. The effect of this mechanism is that
stomata regulate transpiration in that they prevent excessive water loss when this is
threatened. Of course, when the stomata are forced to close, inward diffusion of carbon
dioxide is interrupted.
The opening and closing of stomata
We have seen that, because of the structure of guard cell walls, stomata open when
water is absorbed by the guard cells from the surrounding epidermal cells. Fully turgid
guard cells push into the epidermal cell besides them, and the pore develops.
The guard cells contain chloroplasts (all the other epidermal cells do not), but opening is
not due to the slow build-up of sugar by photosynthesis in these chloroplasts, leading to
the turgor pressure change of opening. Opening is a much quicker process.
Stomatal opening depends on two biochemical changes:
1 Potassium ions (K+ – a cation) are pumped into the guard cell vacuole, from
surrounding cells, by proteins of the cell surface membranes, triggered by light (blue
wavelengths). Calcium ions play a part in this process.
2 Starch, stored in the guard cells, is converted to organic acids, particularly malate.
These anions accompany the K+ cations in the guard cell vacuole.
how stomatal
Question aperture
may vary
9 Examine Figure 14.23.
Suggest why the sunny day
stomatal apertures
stomatal aperture/
(+ adequate moisture)
relative average
arbitrary units
of the plant in the

very dry conditions
differed in both
maximum size and very dry conditions
duration of opening
from those of the
plant with adequate
midnight noon midnight
moisture. time
▲ Figure 14.23 Stomatal opening and environmental conditions

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The accumulation of these substances in the guard cell vacuole causes the water potential
there to become more negative. So, net uptake of water from the surrounding ordinary
14 epidermal cells occurs – making the guard cells extremely turgid (Figure 14.24).
Closing is brought about by the reversal of these steps in the dark. Alternatively closure
occurs when triggered by the stress hormone abscisic acid (ABA), produced in leaf cells
during wilting. We will discuss this situation next.
in the light in the dark

(or if water stress develops due to wilting)
blue light on guard cells
14 Homeostasis
severe wilting of leaf

produces flaccid cells
and therefore
automatic stomatal closure
CO2
cells under water
ABA to stress (slight wilting)
membrane around ABA
guard cells produce ABA
vacuole pumps
K+ ions in from
epidermal cells ABA
K+ K+ ions pumped out
in the guard cells, malate malate K+
of vacuole to other
stored starch is H2O H2O epidermal cells
converted to organic
acids, e.g. malate,
which are pumped
stoma opens stoma closes
into vacuole
malate pumped back into cytoplasm,
water vapour loss in warm, dry air (speeded by wind) converted to sugar, and stored as starch
▲ Figure 14.24 How opening and closing of stomata occurs
Abscisic acid and water stress in the leaf

Abscisic acid (ABA) is a plant growth inhibitor substance. The discovery of growth
inhibitors in plants came from investigations of dormancy in buds and seeds. ABA is
formed in mature leaves, in ripe fruits and seeds, and is present in dormant seeds. It
accumulates in leaves of deciduous trees in late summer, just before their winter buds
become dormant, and also in deciduous tropical plants at the onset of the dry season.
Of particular interest is the fact that ABA is also involved in the closure of stomata
under conditions of drought. Green plants that are experiencing drought produce
ABA in their chloroplasts, including those in the guard cells, and this ‘stress hormone’
triggers stomatal closure. This response involves calcium ions as the ‘second messenger’,
as follows.
ABA triggers release of calcium ions from the cell sap in the guard cell vacuoles into the
guard cell cytosol, via activated calcium ion channels in the tonoplast. Consequently,
the concentration of calcium ions in the cytosol is abruptly increased, and directly
triggers:
1 a sudden efflux of anions such as chloride ions from the cytosol, across the cell
surface membrane, by activated anion channels
2 a sudden efflux of potassium ions from the cytosol, across the cell surface membrane,
by activated potassium ion pumps
3 inhibition of efflux of potassium ions into the guard cells (a feature of the stomatal
opening mechanism).
As a result, the water potential of the guard cells is abruptly raised. It is now higher than
the water potential of the surrounding cells, and a net efflux of water occurs from the
guard cells. The guard cells become flaccid and the pores close.
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SUMMARY
» Homeostasis is the maintenance of a constant variations in intake. Kidney tubules (nephrons)
14
internal environment despite fluctuating external work by pressure filtration of some of the liquid and
conditions. The ability to do this efficiently has soluble components of blood, followed by selective
allowed mammals as a group to live in very reabsorption of useful substances from the filtrate,
diverse habitats. Negative feedback control active secretion of unwanted substances and
mechanisms operate in homeostasis. When adjustments to water and ion content according to
departure from the normal or set value of their status in the body.

conditions within an organism is detected (such » The peptide hormone glucagon stimulates liver
as an abnormal blood sugar level), responses are cells to convert stored glycogen to glucose, work
set in motion which restore normal conditions and by binding to external receptors on liver cells cell
switch off the ‘disturbance’ signal. surface membranes, and indirectly triggering cyclic
» The nervous system and the endocrine system AMP (cAMP) within the cell cytosol. This second
have interconnected roles in coordinating messenger triggers a cascade of reactions in liver
homeostatic mechanisms. The nervous system cells in which the hormone signal is amplified.
consists of receptors (sense organs) linked The impact of glucagon on a liver cell is a three-
to effectors (muscles or glands) by neurones. stage process of cell signalling resulting in the
Hormones are produced in endocrine glands, amplification of the hormone signal. So, from one
transported all over the body in the blood, and activated receptor molecule, perhaps 108 molecules
effect specific target organs. of glucose 1-phosphate are formed from glycogen.
» Blood glucose regulation is essential because cells » Plants carry out gaseous exchange between their
need a more or less constant supply, especially living cells and the air spaces between them, which
brain cells. Too high a glucose level lowers the are continuous throughout the plant. Carbon dioxide
water potential of the blood to the point where the gas enters and oxygen and water vapour leave
circulation takes water by osmosis from tissue fluid the leaves through the pores in stomata. Stomata
and dehydrates cells and tissues. Too low a glucose consist of guard cells surrounding a pore which
level may lead to loss of consciousness and coma. permits this gaseous exchange between leaves and
» The kidney is an organ of excretion and environment. There is a daily rhythm of opening
osmoregulation. In excretion the waste products and closing of guard cells that is over-ruled in the
of metabolism are removed from the blood and event of excess water loss (leading to water stress
made ready for discharge from the body. In within the plant). It is the plant growth regulator,
osmoregulation, the balance of water and solutes in abscisic acid that then triggers premature closure
body fluids is maintained at a constant level despite of stomata, so conserving water.
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14 1 a The mammalian kidney is an organ involved in homeostasis.
Explain what is meant by the term homeostasis. [1]
b Fig. 1.1 shows a section through a kidney.
14 Homeostasis
▲ Fig. 1.1
i With reference to Fig. 1.1, name structures A and B. [2]

ii On a copy of Fig. 1.1, use label lines and letters to label where:
U – ultrafiltration occurs
L – the loop of Henle is found
C – blood urea concentration is low. [3]
c Describe the roles of the hypothalamus and the posterior pituitary in
osmoregulation. [5]
[Total: 11]
2 a After the digestion of carbohydrates in the gut, glucose is absorbed into the
bloodstream and the concentration of blood glucose initially rises. Describe
how a surge in blood glucose is normally regulated by the body and what
happens to the bulk of this metabolite.
b Draw a flow diagram showing the steps by which the concentration of blood
glucose is held constant by a process of negative feedback.
[Total: 20]
3 a Give an illustrated account of the structure of a stoma. [7]
b Outline the mechanism by which the stomatal pore opens. [6]
c How do stress conditions within leaves due to water shortage affect stomatal
opening, and what part do plant growth regulators play in this response? [7]
[Total: 20]
4 a Identify the distinctive roles of the endocrine and nervous systems in
homeostasis, illustrating your answer by reference to the mechanism of
control of blood glucose concentration in mammals. [10]
b Outline the role of a ‘second messenger’ in the impact of a peptide hormone
such as glucagon on a liver cell. [10]
[Total: 20]
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A LEVEL
15.1 Control and coordination in mammals

All the activities of Learning outcomes
multicellular organisms
require coordinating, some
very rapidly and some more 15.1.1 describe the features of the endocrine system with reference to the
slowly. The nervous system hormones ADH, glucagon and insulin (see 14.1.8, 14.1.9 and 14.1.10)
and the endocrine system 15.1.2 compare the features of the nervous system and the endocrine system
provide coordination in 15.1.3 describe the structure and function of a sensory neurone and a motor
mammals. Coordination neurone and state that intermediate neurones connect sensory neurones
systems also exist in plants.
and motor neurones
15.1.4 outline the role of sensory receptor cells in detecting stimuli and
stimulating the transmission of impulses in sensory neurones
15.1.5 describe the sequence of events that results in an action potential in a
sensory neurone, using a chemoreceptor cell in a human taste bud as an
example
15.1.6 describe and explain changes to the membrane potential of neurones,
including: how the resting potential is maintained, the events that occur
during an action potential, how the resting potential is restored during the
refractory period
15.1.7 describe and explain the rapid transmission of an impulse in a myelinated
neurone with reference to saltatory conduction
15.1.8 explain the importance of the refractory period in determining the
frequency of impulses
15.1.9 describe the structure of a cholinergic synapse and explain how it
functions, including the role of calcium ions
Starting points
★ The endocrine system is a slower system that controls long-term changes.
★ The nervous system provides fast communication between receptors and
effectors.
★ Transmission between neurones takes place at synapses.

The need for communication systems
The ability to detect change and to make responses is essential for the survival of living
things. It is as much a feature of single-celled organisms as it is of flowering plants and
mammals. We see this when an Amoeba detects a suitable food organism and captures it
by phagocytosis.
Large and complex organisms detect changes in the external environment as well as
changes within the body. They need to communicate this information to parts of the
body where appropriate responses will be made.
We call changes that bring about responses stimuli. The stimulus is detected by a
receptor and an effector brings about a response. Since response often occurs in
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a different part of the body, efficient internal communication is also essential. In
mammals, internal communication involves both the endocrine (hormone-producing)
15 and nervous systems. We will examine these next.
Introducing the endocrine system

Hormones are chemical messengers. They are produced and secreted from the cells
in glands known as ductless or endocrine glands. These contain capillary networks
and specialised secretory cells that make and release hormones. Hormones are released
from the cells of the ductless gland, directly into the blood stream, when stimulated to
do so. Hormones are then transported indiscriminately about the body via the blood
circulation system, but they act only at specific sites, appropriately called target organs.
Cells of the target organ possess specific receptor molecules on the external surface of
their cell surface membrane to which the hormone molecules bind. A hormone typically
works by triggering changes to specific metabolic reactions in their target organs.
Although present in small quantities, hormones are extremely effective in the control
and co-ordination of several body activities. The position of the main endocrine glands
and the hormones produced are summarised in Figure 15.1.
hypothalamus:
pituitary gland (secretes hormones
– anterior controlling activity
– posterior: ADH of the anterior
pituitary)
thyroid gland
thymus gland
(this is NOT an
endocrine gland)
pancreas (islets
adrenal glands of Langerhans):
insulin, glucagon
ovaries/testes:
sex hormones,
oestrogen and
testosterone
▲ Figure 15.1 The human endocrine system
Hormones circulate in the bloodstream only briefly because in the liver they are
Question continually being broken down. Any breakdown products no longer of use to the
1 Hormones, on body are excreted in the kidneys. So, long-acting hormones must be secreted into the
secretion, are bloodstream continuously to be effective – and they are.
transported all
Antidiuretic hormone (ADH) is involved in osmoregulation (see page 308); it is produced in
over the body.
Explain how the the hypothalamus and released into the capillary network in the posterior pituitary gland.
effects of hormones Glucagon and insulin are hormones involved in the control of blood glucose
are restricted to concentration (see page 296); they are secreted by α and β cells of the islets of
particular cells or Langerhans in the pancreas.
tissues.
The structure of endocrine glands can be contrasted with that of other glands in our body
which deliver their secretions through tubular ducts, such as the salivary glands in the
mouth and sweat glands in the skin. These ducted glands are called exocrine glands. Their
secretions pass out of the gland via ducts and they have altogether different roles in the body.
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Hormonal control of body function mostly works by causing specific changes in
metabolism or development, often over an extended period of time. The nervous system,
on the other hand, is concerned with quick, precise communication. These contrasting
systems are coordinated by the brain. Our nervous system and hormones work together.
15
Introducing the nervous system
The nervous system is built from specialised nerve cells called neurones. Neurones are
grouped together to form the central nervous system, which consists of the brain and
spinal cord (Figure 15.2). To and from the central nervous system run nerves of the

peripheral nervous system. Communication between the central nervous system and
all parts of the body occurs via neurones in these nerves.
Specialised nerve cells brain internal

external
(neurones) are stimuli
stimuli
organised into central
nervous system and spinal cord
peripheral nerves receptors
central nervous system
linking sense organs, (sense organs)
muscles and glands
with the brain or
spinal cord.
nerves
coordination impulses transmitted
of responses by the neurones of the
by the brain nervous system
effector organs
peripheral
e.g.
nervous system
musles glands
feedback
information
responses
▲ Figure 15.2 The organisation and coordination of the mammalian nervous system
Neurones – structure and function

Each neurone has a cell body containing the nucleus and the bulk of the cytoplasm.
From the cell body, extremely fine cytoplasmic processes run. Many of these
processes are very long indeed. They are specialised for the transmission of information
in the form of impulses. Impulses are transmitted at speeds between 30 and 120
metres per second in mammals, so nervous coordination is extremely fast and
responses are virtually immediate. Another feature of the nerve impulse is that it
travels to particular points in the body. Consequently, the effects of impulses are
localised rather than diffuse. (This makes communication by nerves different from that
by hormones, as we shall see.)
The three types of neurone are shown in Figure 15.3, overleaf.
Question
2 Compare motor, » Motor neurones have a cell body that lies within the brain or spinal cord. Many
sensory and highly-branched cell processes extend from the cell body. These are called dendrites.
intermediate Dendrites receive impulses from other neurones and conduct them towards the cell
neurones by means body. A single long axon transmits impulses away from the cell body. The function of
of a concise table. a motor neurone is to transmit impulses from the central nervous system to effector
organs, such as muscles or glands.
» Intermediate neurones (also known as relay or interneurones) have numerous, short
fibres. Each fibre is a thread-like extension of a nerve cell. Intermediate neurones occur
in the central nervous system. They connect sensory neurones and motor neurones.
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» Sensory neurones have a single long dendron, which brings impulses towards the
cell body, and a single axon which carries impulses away from the cell body. Sensory
15 neurones transmit impulses from receptors to the spinal cord or brain.
Surrounding the neurones there are different types of supporting cells called glia cells.
These are also an important part of the nervous system. In the brain and spinal cord
there are several types of glia cells. In the peripheral nervous system, the axons of
many neurones are enclosed by glia cells called Schwann cells. These wrap themselves
around the axon with many layers of cell surface membrane, forming a structure called
a myelin sheath (Figure 15.3). The sheath consists largely of lipid with some protein.
Between each pair of Schwann cells is a tiny, uncovered junction in the myelin sheath,
called a node of Ranvier. The myelin sheath and its junctions help increase the speed at
which impulses are conducted – a point we will return to shortly.
motor neurone intermediate neurone sensory neurone
many fibres
dendrites
dendrites cell body dendrites
axon
dendron dendron
cell body
nucleus
nucleus
cytoplasm
direction
axon of
nucleus
impulse
axon
direction
of
myelin sheath
impulse cell body
node of Ranvier direction

of
axon
impulse
junction between two sheath

cells = node of Ranvier
myelin sheath
formed by Schwann cell
wrapping itself around the
axon
axon (or dendron)
▲ Figure 15.3 Neurones of the nervous system

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Organisation among neurones – reflex arcs and reflex action
The transmission of nerve impulses is not a haphazard process. It involves organised
pathways among the neurones. These pathways are called reflex arcs. The reflex arc 15
consists of a receptor, which may be a sensory organ, connected by neurones to an
effector, which may be a muscle or gland. A generalised reflex arc is shown in Figure 15.4.
sensory neurone stimulus
e.g. mechanical
pressure
receptor

e.g. sense
organ
effector
intermediate neurone (e.g. muscle)
motor neurone
▲ Figure 15.4 The layout of a reflex arc: the structural basis of reflex action
How does a reflex arc work?

The action begins when a sense organ detects a stimulus, which is a form of energy
such as sound, light or mechanical pressure. This may become an impulse transmitted
by a neurone that serves that sense cell. Once generated, the impulse is transmitted
along dendrons and axons of a sequence of neurones of the reflex arc to an effector
organ. When it arrives at the effector, the impulse causes a response – for example,
it may cause a muscle to contract or a gland to secrete.
EXTENSION
Reflex arcs and the nervous system » impulses may originate in the brain and be
conducted to effector organs.
What has just been described is the simplest form of
response in the nervous system. In mammals there is a Consequently much activity is initiated by the brain,
complex nervous system. Many neurones connect reflex rather than being simply a response to external stimuli.
arcs with the brain. The brain contains a highly organised Also, reflex actions may be overruled by the brain and
mass of intermediate neurones, connected with the rest of the response modified (as when we decide not to drop
the nervous system by motor and sensory neurones. an extremely hot object because of its value).
With a nervous system of this type, complex patterns So, the nervous system of mammals has roles in both
of behaviour are common, in addition to many reflex quick, precise communication between the sense
actions. This is because: organs that detect stimuli and the muscles or glands
that cause changes and in the complex behaviour
» impulses that originate in a reflex arc also travel to
patterns that mammals display.
the brain
Sensory receptors and the conversion of energy into impulses

All cells are sensitive to changes in their environment, but sense cells are specialised to
detect stimuli and to respond by producing an impulse (an action potential). Specialised
sense cells are called receptors. Different types of sensory receptors exist in the body.
The property of a sense cell is to transfer the energy of a particular type of stimulus
into the electrochemical energy of an impulse, which is then conducted to other parts
of the nervous system. The stimulus that the sense cell responds to is some form
of energy, mechanical, chemical, thermal or light (photic). The sense organs of
mammals are listed in Table 15.1 under headings of the stimuli they respond to.
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Sense data (form of energy) Type of receptor Location in the body
15 Mechanoreceptors: respond to mechanical stimulation

Light touch Touch receptors Mostly in dermis of skin
Touch and pressure Touch and pressure receptors Dermis of skin
Movement and position Stretch receptors, e.g. muscle Skeletal muscle
spindles, proprioceptors
Sound waves and gravity Sensory hair cells Cochlea and other parts
of the inner ear
Blood pressure Baroreceptors Aorta and carotid artery

Thermoreceptors: respond to thermal stimulation
Temperature change in the skin Nerve endings Dermis of skin
Internally Cells of hypothalamus Brain
Chemoreceptors: responding to chemical stimulation
Chemicals in the air Sense cells of olfactory Nose
Question epithelium
3 Use Table 15.1 to list Taste Taste buds Tongue
the various types of Blood oxygen and carbon Carotid body Carotid artery
stimuli (sense data) dioxide concentrations and pH
that originate from
Osmotic concentration of the Osmoregulatory centre in Brain
conditions within
blood hypothalamus
the human body
that are detected by Photoreceptors: respond to electromagnetic stimulation
particular receptors. Light Rod and cone cells of retina Eye
▲ Table 15.1 The sense organs of mammals
Chemoreceptors
Chemoreceptors, specialised sensory receptors in our sense organs, recognise the
chemical stimuli by which organisms collect information about their internal and
external environments.
The senses of taste and smell are the most familiar examples of chemoreception in
humans. Humans have approximately 100,000 chemoreceptor cells in taste buds,
located on the upper surface of the tongue, soft palate, upper oesophagus and epiglottis.
The sense of smell also relies on chemoreceptors located in the nose and these play a
crucial role in distinguishing more subtle differences in taste.
Taste buds are composed of a cluster of between 50 and 150 columnar taste receptor
cells grouped together a bit like a bunch of bananas. Each taste bud can detect sweet,
sour, salty, umami or bitter tastes. Slender processes (microvilli)
taste pore
extend from the outer ends of the receptor cells through the
taste pore (Figure 15.5). At their inner end, each taste receptor
mucous cell synapses (connects) with an afferent nerve that transmits
membrane information to the brain.
of tongue
microvilli
Dissolved chemicals from food enter the taste bud through the
taste pore and bind to the receptor cells, causing a change in
sensory the shape of the chemoreceptor protein on the cell surface. This
cell change in shape causes chemical-gated sodium channels in the
cells to open, resulting in an influx of sodium ions into the cells
and causing the cell membrane to depolarise. This depolarisation
nerve is transmitted to the taste neurones, resulting in an action
fibres potential that is ultimately transmitted to the medulla oblongata
▲ Figure 15.5 The structure and function of a taste bud in the brain, where it is recognised as a specific taste.
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Transmission of an impulse
An impulse is transmitted along nerve fibres, but it is not an electrical current that flows
along the ‘wires’ of the nerves. Rather, the impulse is a momentary reversal in electrical 15
potential difference in the membrane, caused by the rapid movements of sodium and
potassium ions into and out of the axon.
The resting potential

A neurone that is not transmitting an impulse is said to be at rest. Actually, this not the
case; during the ‘resting’ interval between the transmission of impulses, the membrane of a

neurone actively creates and maintains an electrical potential difference between the inside
and the outside of the fibre. The result is that, in a ‘resting’ neurone there is a potential
difference between the inside and the outside of the fibre of about −70 mV. (The discovery
of the resting potential came from the use of an external and internal microelectrode on an
isolated axon, the amplification of the signal and its display on a cathode ray oscilloscope).
Two processes together produce the resting potential difference across the neurone
membrane.
» There is active transport of potassium ions (K+) in across the membrane and of
sodium ions (Na+) out across the membrane. The ions are transported by a sodium–
potassium pump, with transfer of energy from ATP. So potassium and sodium ions
gradually concentrate on opposite sides of the membrane. Of course, this in itself
makes no change to the potential difference across the membrane.
» There is also facilitated diffusion of potassium ions out and sodium ions back in.
The important point here is that the membrane is far more permeable to potassium
ions flowing out than to sodium ions returning. This causes the tissue fluid outside
the neurone to contain many more positive ions than are present in the cytoplasm
inside. As a result, the inside becomes more and more negatively charged compared
with the outside; the resting neurone is said to be polarised. The difference in
charge, or potential difference, is about −70 mV. This is known as the resting
potential. Figure 15.6 is a summary of how it is set up.
tissue fluid outsidecell surface membrane of axon cytoplasm of axon
+
+ +
–
+ – – +
– +–
+ – – +
–
+ +
+
K+/Na+ pumps ion diffusion proteins outcome: more positively
(active transport) (facilitated diffusion) charged ions outside than inside
ATP Na+ ion-diffusion protein –

active transport facilitated
slightly permeable
K+ ions diffusion
to Na+ ions
pore open membrane
ADP + Pi to K+ ions protein
inside inside
lipid axon
bilayer membrane
outside outside
protein pump K+ ion-diffusion pore open
Na+ ions to Na+ ions
protein – highly
permeable
to K+ ions
▲ Figure 15.6 The establishment of the resting potential

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The action potential
15 The next event in a neurone, sooner or later, is the passage of an impulse. An impulse
or action potential is triggered by a stimulus received at a receptor cell or sensitive
nerve ending (Figure 15.7).
In the action potential, the energy transferred by this stimulus causes a temporary
and local reversal of the resting potential. The result is that the membrane is briefly
depolarised at this point. How does this happen?
The change in potential across the membrane occurs through pores in the membrane.
They are called ion channels because they can allow ions to pass through. One type
of channel is permeable to sodium ions and another to potassium ions. These channels
are globular proteins that span the entire width of the membrane. They have a central
pore with a gate which can open and close – they are gated channels. During a resting
potential these channels are all closed.
The energy of the stimulus first opens the gates of the sodium channels in the cell
surface membrane. This allows sodium ions to diffuse in, down their electrochemical
gradient. This influx of sodium ions is very rapid indeed. So the cytoplasm inside the
neurone fibre quickly becomes progressively more positive with respect to the outside.
This charge reversal continues until the potential difference has altered from −70 mV to
+40 mV. At this point, an action potential has been created in the neurone fibre.
sodium channels potassium channels motor neurone
(gated) (gated) direction of impulse
K+
K+ K+
2 4
the gates are sometimes

referred to as
voltage-gated channels
Na+ Na+ Na+

action
part of axon potential
(cut open)
resting potential
+ + + + + + + – + + + + + + +
+ +
– – – – – – – + – – – – – – –
+ – – +
– –
– – – – – – – + – – – – – – + – – +
–
+ +
+ + + + + + + – + + + + + + +
depolarisation Ion movements during the action

due to Na+ entry potential:
1 During the resting potential the ion channels for

+40 4 Na+ ions and K + ions are both closed.
change in potential difference in
2 Na+ channels open and Na+ ions rush in
membrane potential difference/mV
+30
cell surface membrane of neurone
(by diffusion).
during the passage of an action +20
3 3 Interior of axon becomes increasingly more
potential +10 positively charged with respect to the outside.
0 4 Equally suddenly, Na+ channels close at the
same moment as K+ channels open and K + ions
–10 5 rush out (by diffusion).
–20 5 Interior of axon now starts to become less
–30 positive again.
passage of action potential as a –40
6 Na+/K+ pump starts working, together with
‘spike’ running along the length facilitated diffusion, so that the resting potential
–50 2 is re-established.
of the neurone resting
–60
1 6 potential
–70
0 1 2 3 4 5
time/ms
▲ Figure 15.7 The action potential
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The action potential then travels along the whole length of the neurone fibre. At any
one point it exists for only two thousandths of a second (2 milliseconds), before the
membrane starts to re-establish the resting potential. So action potential transmission is
exceedingly quick – an example of positive feedback, in fact.
15
Questions Almost immediately an action potential has passed, the sodium channels close and
the potassium channels open. So potassium ions can exit the cell, again down an
4 Distinguish between electrochemical gradient, into the tissue fluid outside. This causes the interior of the
positive and negative neurone fibres to start to become less positive again. Then the potassium channels
feedback. also close. Finally, the resting potential of −70 mV is re-established by the action of the

5 What is the source of sodium–potassium pump and the process of facilitated diffusion.
energy used to
a establish the The refractory period
resting potential For a brief period, following the passage of an action potential, the neurone fibre is not
b power an action excitable. This is the refractory period. It lasts only 5–10 milliseconds in total. During
potential? this time, firstly there is a large excess of sodium ions inside the neurone fibre and
6 Why is an axon further influx is impossible. As the resting potential is progressively restored, however,
unable to conduct an it becomes increasingly possible for an action potential to be generated again. Because
impulse immediately of this refractory period, the maximum frequency of impulses is between 500 and
after an action 1000 per second.
potential has been
conducted? The ‘all or nothing’ principle
Obviously stimuli are of widely different natures, such as the difference between a
light touch and the pain of a finger hit by a hammer. A stimulus must be at or above
a minimum intensity, known as the threshold of stimulation, in order to initiate
an action potential at all. Either a stimulus depolarises the membrane sufficiently to
reverse the potential difference in the cytoplasm (−70 mV to +40 mV), or it does not.
If not, no action potential is generated. With all sub-threshold stimuli, the influx of
sodium ions is quickly reversed, and the resting potential is re-established.
However, as the intensity of the stimulus increases the frequency at which action
potentials pass along the fibre increases. (Note that individual action potentials are all
of standard amplitude.) For example, with a very persistent stimulus, action potentials
pass along a fibre at an accelerated rate, up to the maximum possible permitted by the
refractory period. This means the effector (or the brain) recognises the intensity of a
stimulus from the frequency of action potentials (Figure 15.8).
stimuli below the brief stimulus stronger, more persistent much stronger stimulus:
threshold value: just above stimulus has stimulated almost the
not sufficient to threshold maximum frequency of
reverse polarity of value: impulses
the membrane to needed to
+40 mV depolarise the
sensory cell
membrane
and trigger
an impulse
no action potential
stimulus stimulus stimulus stimulus stimulus

starts stops starts stops
▲ Figure 15.8 Weak and strong stimuli and the threshold value
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Speed of conduction of the action potential
15 We noted earlier that the presence of a myelin sheath affects the speed of transmission of
the action potential. The junctions in the sheath, known as the nodes of Ranvier, occur
at 1–2 mm intervals. Only at these nodes is the axon membrane exposed. Elsewhere
along the fibre, the electrical resistance of the myelin sheath prevents depolarisations.
Consequently, the action potentials are forced to jump from node to node. This is called
saltatory conduction (from the Latin saltare meaning ‘to leap’) (Figure 15.9). This is an
advantage, as it greatly speeds up the rate of transmission.
Not all neurones have myelinated fibres. In fact, non-myelinated dendrons and axons
Question
are common in non-vertebrate animals. Here, transmission is normally much slower,

7 Why do myelinated because the action potential flows steadily, all along the fibres. However, among non-
fibres conduct myelinated fibres it is a fact that large diameter axons transmit action potentials much
impulses faster than more speedily than do narrow ones. Certain non-vertebrates like the squid and the
non-myelinated earthworm have giant fibres, which allow fast transmissions of action potentials (not as
fibres of the same fast as in myelinated fibres, however). We saw that the original investigation of action
size? potentials was carried out on such giant fibres.
direction of impulse
Na+ out Na+ in localised circuit K+ out
Na+ out axon Na+ in myelin K+ out

node of Ranvier sheath
▲ Figure 15.9 Saltatory conduction
Synapses – the junctions between neurones

Where two neurones meet they do not actually touch. A tiny gap, called a synapse, is
the link point between neurones. Synapses consist of the swollen tip (synaptic knob)
of the axon of one neurone (the presynaptic neurone) and the dendrite or cell body of
another neurone (the postsynaptic neurone). Between these is the synaptic cleft, a gap
of about 20 nm (Figure 15.10).
The practical effect of the synaptic cleft is that an action potential cannot cross it. Here,
transmission occurs by particular chemicals, known as transmitter substances. These
substances are all relatively small, diffusible molecules. They are produced in the Golgi
apparatus in the synaptic knob and held in tiny vesicles before use.
Acetylcholine (ACh) is a commonly occurring transmitter substance. The neurones that
release acetylcholine are known as cholinergic neurones. Another common transmitter
substance is noradrenaline (released by adrenergic neurones). In the brain the
commonly occurring transmitters are glutamic acid and dopamine.
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axon of
presynaptic
15
direction of
neurone
transmission
myelin sheath
endoplasmic
reticulum
Golgi
apparatus synaptic knob

mitochondrion
vesicles containing
transmitter
substance
presynaptic
synaptic membrane
cleft
postsynaptic
membrane
synaptic cleft gap is

tiny, typically 20 nm
Figure 15.10 synaptic knob
A synapse in of postsynaptic
section neurone TEM of a synapse (×100 000)
Steps to synapse transmission

It may help to follow the steps in Figure 15.11, overleaf.
1 The arrival of an action potential at the synaptic knob opens calcium ion (Ca2+)
channels in the presynaptic membrane. Calcium ions flow in from the synaptic cleft.
2 The calcium ions cause vesicles of transmitter substance to fuse with the presynaptic
membrane and they release a transmitter substance into the synaptic cleft.
3 The transmitter substance diffuses across the synaptic cleft and binds with a
receptor protein.
In the postsynaptic membrane there are specific receptor sites for each transmitter
Question substance. Each of these receptors also acts as a channel in the membrane which
8 In the synaptic knob, allows a specific ion (sodium, potassium or some other ion) to pass. The attachment
what is the role of: of a transmitter molecule to its receptor instantly opens the ion channel.
a the Golgi When a molecule of the transmitter substance attaches to its receptor site, sodium
apparatus ion channels open. As the sodium ions rush into the cytoplasm of the postsynaptic
b mitochondria? neurone, depolarisation of the postsynaptic membrane occurs. As more and more
molecules of the transmitter substance bind, it becomes increasingly likely that
depolarisation will reach the threshold level. When it does, an action potential
is generated in the postsynaptic neurone. This process of build-up to an action
potential in postsynaptic membranes is called facilitation.
4 The transmitter substance on the receptors is quickly inactivated. For example,
the enzyme cholinesterase hydrolyses acetylcholine to choline and ethanoic acid.
These molecules are inactive as transmitters. This reaction causes the ion channel of
the receptor protein to close and so allows the resting potential in the postsynaptic
neurone to be re-established.
5 Meanwhile, the inactivated products of the transmitter re-enter the presynaptic
knob, are resynthesised into transmitter substance and packaged for reuse.
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how a cholinergic
synapse works
15 structure of Ca 2+ channels
in presynaptic membrane
(enlarged)
1 impulse arrives
at synapse, and 5 reformation of Ca2+
triggers Ca2+ transmitter
ion entry substance vesicles
Ca2+
ions
4 enzymic
inactivation of
transmitter
2 transmitter
substance
released,
diffuses to transmitter substance cycle
receptors of
postsynaptic
membrane reformation
using energy
from ATP
1 permeability 5
to Ca2+
increases
3 transmitter substance
binds, triggering entry of
Na+ ions, and action potential re-entry
in postsynaptic membrane
release
2 diffusion
diffusion enzymic
3
inactivation 4
binding
Na+ channel opening

(impulse generated)
▲ Figure 15.11 Chemical transmission at a synapse
Why have synapses between neurones?

Since synapses have the disadvantage of very slightly slowing down the transmission of
action potentials, we may assume they also provide distinct advantages to the operation
of nervous communication in organisms. In fact there are a number of advantages.
» They filter out low-level stimuli of limited importance.
» They protect the effectors (muscles and glands) from over-stimulation, since
continuous transmission of action potentials eventually exhausts the supply of
transmitter substances for a period of time. This is called synapse fatigue.
» They facilitate flexibility of response by the central nervous system, particularly by
the brain.
» They allow integration of information since the postsynaptic neurone may receive
action potentials from different types of neurone. Both excitatory presynaptic
neurones and inhibitory presynaptic neurones exist. The postsynaptic neurone
summates all the action potentials, thereby integrating action potentials from more
than one source neurone or sense organ, for example.
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EXTENSION
An alternative type of synapse
15
In this section on synapses, it is an excitatory synapse that has been described.
That is, the incoming action potential excited the postsynaptic membrane and
generated an action potential that was then transmitted along the postsynaptic
neurone. Some synapses, however, have the opposite effect. These are known as
inhibitory synapses.
15.1 continued…Neuromuscular junctions and muscle contraction

EXTENSION
Drugs may interfere with the activity of synapses
Some drugs amplify the processes of synaptic transmission, in effect they increase
postsynaptic transmission. Nicotine and atropine have this effect.
Other drugs inhibit the processes of synaptic transmission, in effect decreasing
synaptic transmission. Amphetamines and beta-blocker drugs have this effect.
15.1 continued…Neuromuscular junctions and muscle

contraction
Learning outcomes
By the end of this topic, you wll be able to:
15.1.10 describe the roles of neuromuscular junctions, the T-tubule system and
sarcoplasmic reticulum in stimulating contraction in striated muscle
15.1.11 describe the ultrastructure of striated muscle with reference to
sarcomere structure using electron micrographs and diagrams
15.1.12 explain the sliding filament model of muscular contraction including the
roles of troponin, tropomyosin, calcium ions and ATP
Starting point
★ Motor nerve endings make connections with muscle fibres and trigger muscle
contraction.
The structures of striated muscle

Skeletal muscle fibres appear striped under the light microscope, so skeletal muscle is also
known as striated muscle. Striated muscle consists of bundles of muscle fibres (Figure 15.12,
overleaf). The remarkable feature of a muscle fibre is the ability to shorten to half or even
a third of the relaxed or resting length. Actually, each fibre is itself composed of a mass of
myofibrils, but we need the electron microscope to see this important detail.
The ultrastructure of skeletal muscle

Skeletal muscle fibres are multinucleate and contain specialised endoplasmic reticulum.
By electron microscope we can see that each muscle fibre consists of very many parallel
myofibrils within a plasma membrane known as the sarcolemma, together with cytoplasm.
The cytoplasm contains mitochondria packed between the myofibrils. The sarcolemma
infolds to form a system of transverse tubular endoplasmic reticulum (referred to as the
T-tubule system), and all parts of the sarcoplasmic reticulum. This is arranged as a network
around individual myofibrils. The arrangements of myofibrils, sarcolemma and mitochondria,
surrounded by the sarcoplasmic membrane, are shown in Figure 15.13 (overleaf).
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skeletal muscle cut to show bundles of fibres
15 bundle of thousands
of muscle fibres
tendon
connective tissue
alternating light and dark bands

of muscle fibres (when viewed
microscopically)
individual
each muscle fibre contains muscle fibre
several nuclei (i.e. a syncytium)
each fibre consists
of a mass of myofibrils
▲ Figure 15.12 The structure of skeletal muscle
electron micrograph of TS through part stereogram of part of a single muscle fibre

of a muscle fibre, HP (×36 000)
sarcoplasmic
membrane
sarcoplasm (cytoplasm of
muscle cell)
myofibril
mitochondrion
sarcoplasmic reticulum
with T-tubules
▲ Figure 15.13 The ultrastructure of a muscle fibre
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The striped appearance of skeletal muscle is due to an interlocking arrangement of two
types of protein filaments, known respectively as thick and thin filaments – they make
up the myofibrils. These protein filaments are aligned, giving the appearance of stripes
(alternating light and dark bands). This is shown in the more highly magnified electron
15
micrograph and interpretive drawing in Figure 15.14.
Electron micrograph of an individual sarcomere (×34000)
individual sarcomere
Z line Z line

myosin protein
(thick filament in the
with ‘heads’) M line
Z line light band dark band light band Z line
▲ Figure 15.14 The ultrastructure of a myofibril
The thick filaments are made of a protein called myosin. They are about 15 nm in
diameter. The longer, thin filaments are made of another protein, actin. Thin filaments
are about 7 nm in diameter, and are held together by transverse bands, known as Z
lines. Each repeating unit of the myofibril is, for convenience of description, referred to
as a sarcomere. So we can think of a myofibril as consisting of a series of sarcomeres
attached end to end.
How a motor nerve ending makes connection with a

muscle fibre
Striated muscle fibres are innervated by a motor neurone nerve ending, at a structure
known as a motor end plate or neuromuscular junction (Figure 15.15, overleaf). This is
a special type of synapse, but the transmitter substance is the familiar acetylcholine.
On arrival of an action potential at the neuromuscular junction, vesicles of acetylcholine
are released and the transmitter molecules bind to receptors on the sarcoplasm (this is
the plasma membrane of the muscle fibre). This triggers the release of calcium ions from
the sarcoplasmic reticulum, into the cytoplasm around the myofibrils, via the T-tubule
system. These calcium ions then remove the blocking molecules on binding sites of the
actin filaments (see below). This starts the contraction process. When action potentials
stop arriving at the muscle fibres, calcium ions return to the sarcoplasmic reticulum and
the binding sites are again covered by blocking molecules.
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axon
15
myelin sheath
(stained dark in
photomicrograph)
mitochondrion
vesicle presynaptic membrane

synaptic cleft
postsynaptic sarcolemma
membrane
sarcoplasm
myofibril
▲ Figure 15.15 The structure of a neuromuscular junction
Skeletal muscle contracts by sliding of the filaments

When skeletal muscle contracts, the actin and myosin filaments slide past each other,
in response to nervous stimulation, causing shortening of the sarcomeres (Figure 15.16).
This occurs in a series of steps, sometimes described as a ratchet mechanism. A great
deal of ATP is used in the contraction process.
Shortening is possible because the thick filaments are composed of many myosin
molecules, each with a bulbous head, which protrudes from the length of the myosin
filament. Along the actin filament are a complementary series of binding sites to
which the bulbous heads fit. However, in muscle fibres at rest, the binding sites carry
blocking molecules (a protein called tropomyosin), so binding and contraction are
not possible.
Calcium ions play a critical part in the muscle fibre contract mechanism, together with
the proteins tropomyosin and troponin. The contraction of a sarcomere is described in
the following four steps.
1 The myofibril is stimulated to contract by the arrival of an action potential. This
triggers release of calcium ions from the sarcoplasmic reticulum, which surround
the actin molecules. Calcium ions now react with an additional protein present
(troponin) which, when so activated, triggers the removal of the blocking molecule,
tropomyosin. The binding sites are now exposed.
2 Each bulbous head to which ADP and Pi are attached (called a charged bulbous head)
reacts with a binding site on the actin molecule beside it. The phosphate group (Pi) is
shed at this moment.
3 The ADP molecule is then released from the bulbous head, and this is the trigger for
the rowing movement of the head, which tilts at an angle of about 45°, pushing the
actin filament along. At this step, the power stroke, the myofibril has been shortened
(contraction).
4 Finally, a fresh molecule of ATP binds to the bulbous head. The protein of the
bulbous heads includes the enzyme ATPase, which catalyses the hydrolysis of ATP.
When this reaction occurs, the ADP and inorganic phosphate (Pi) formed remain
attached, and the bulbous head is now ‘charged’ again. The charged head detaches
from the binding site and straightens.
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stretched/relaxed:
electron
15
micrograph
thick filament = myosin thin filament = actin
interpretive
drawing

contracted:
electron
micrograph
interpretive
drawing
▲ Figure 15.16 Muscle contraction of a single sarcomere
Question 9 Explain the relationship to a muscle of:

a a muscle fibre
b a myofibril
c a myosin filament.
This cycle of movements is shown is Figure 15.17, overleaf. The cycle is repeated many
times per second, with thousands of bulbous heads working along each myofibril. ATP
is rapidly used up, and the muscle may shorten by about 50 per cent of its relaxed
length. However, when the action potential stimulation stops, the muscle cell relaxes.
Now, the filaments slide back to their original positions. Ion pumps in the sarcoplasmic
reticulum pump calcium ions back inside, and so the calcium ion concentration
surrounding the myosin filaments falls. Blockage of binding sites by tropomyosin
is restored.
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Arrival of nerve impulse releases Ca2+ from the sarcoplasmic reticulum. Ca2+ ions cause removal
of blocking molecule from binding sites. Each myosin molecule has a bulbous head that reacts
15 with ATP → ADP + Pi which remain bound.
binding site exposed
actin filament
The mechanism of muscle contraction:
myosin head ADP
• The myofibril is stimulated to contract
P by nervous stimulation. This triggers
cross-bridge
release of calcium ions from the

myosin filament sarcoplasmic reticulum, around the
actin molecules. Calcium ions react with
the blocking molecules, removing them
so the binding sites are now exposed.
1 myosin head (with ADP + Pi) binds

to exposed binding site on actin
molecule, and the Pi ion is released
ADP P
• Each bulbous head to which ADP and
Pi is attached (called a charged myosin
head) reacts with a binding site on the
actin molecule next to it. The phosphate
ion (Pi) is shed at this moment.
2 release of the ADP triggers
movement of myosin, by a
‘rowing action’, the power
power stroke ADP
stroke. The actin filament is
moved
• Then the ADP molecule is released

from the myosin head. This is the
trigger for the ‘rowing movement’ of
the head, which tilts by an angle of
about 45°, pushing the actin filament
along. At this step, the power stroke,
the myofibril has been shortened
(contraction).
ATP
4 cycle is repeated at binding

site further along the actin molecule
• Finally, a fresh molecule of ATP binds

to the myosin head. The protein of the
myosin head includes the enzyme
ATPase, which catalyses the hydrolysis of
3 ATP combines with myosin head and is ATP ATP. When this reaction occurs, the ADP
hydrolysed to ADP + Pi, releasing head, and inorganic phosphate (Pi) formed
and allowing cross-bridge to straighten remain attached. The myosin head is now
‘charged’ again. The charged head
detaches from the binding site and
straightens.
5 when nerve stimulation of muscles ceases, Ca2+

ions return to the sarcoplasmic reticulum and the
binding sites become blocked again
▲ Figure 15.17 The sliding filament hypothesis of muscle contraction
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15.2 Control and coordination in plants
Learning outcomes
15
15.2.1 describe the rapid response of the Venus fly trap to stimulation of hairs
on the lobes of modified leaves and explain how the closure of the trap is
achieved
15.2.2 explain the role of auxin in elongation growth by stimulating proton
pumping to acidify cell walls

15.2.3 describe the role of gibberellin in the germination of barley
(see 16.3.4)
Starting points
★ Plant coordination systems involve rapid responses as in the case of
the Venus fly trap, but also complex interactions between plant growth
regulators, such as auxin and gibberellin.
★ Plants respond quite differently to different concentrations of plant growth
regulators.
The responding plant – communication and control in

flowering plants
Sensitivity is a characteristic of all living things, but the responses of plants and
animals differ. Most plants are anchored organisms, growing in one place and
remaining there, even if the environment is not wholly favourable. As a result, plant
responses are often less evident than those of animals, but they are no less important to
the plant. Plants are highly sensitive to environmental clues and external and internal
stimuli, and respond to changes (Figure 15.18). Yet plants have no nervous system and
no muscle tissue. Consequently, plant sensitivity may lead to responses less dramatic
than those of animals.
Rapid movements by plants are extremely rare (but see Figure 15.18c); plant
responses are mostly growth movements. An example of this is the growth of young
stems towards light. Another is the growth of the main root down into the soil in
response to gravity. Occasionally, movements are due to turgor changes (Figure
15.18d). However, there is no doubt that plant responses are also precise and carefully
regulated responses.
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a) The response of a plant stem to light b) Leaf fall in a woody plant of temperate climate
lateral mature, active leaf of woody twig
15 bud
plants grown in the dark have
‘bolted’ stem, small leaves, and
are pale yellow IAA from
stem apex and
from leaf tissue
junction of leaf base and
stem in longitudinal section ageing leaf
prior to
IAA production
plants grown in the light abscission

at stem apex and
are short, sturdy and and leaf fall
in leaf slows
dark green
and eventually
stops
vascular
bundles
abscission
layer ethene production commences in ageing
leaves – and is antagonistic to the effects
of IAA, bringing about the formation of the
abscission layer; leaf fall follows
c) The response of the sensitive plant Mimosa pudica to touch d) Closure of a leaf of the canivorous plant
Drosera rotundifolia, to trap an insect
▲ Figure 15.18 Examples of plant sensitivity and responses
Among the internal factors that play a part in plant sensitivity, the most important are the
substances we call plant growth regulators and their effects. There are five major types
of compound naturally occurring in plants that we call growth regulators. The effects of
these chemicals are rather different from those of animal hormones (see Table 15.2).
Plant growth regulators:
» occur in very low concentrations in plant tissues, so sometimes it is hard to
determine their precise role
» are produced in a variety of tissues, rather than in discrete endocrine glands
» often interact with each other in controlling growth and sensitivity – some interact
to reinforce each other’s effects (synergism), others oppose each other’s effects
(antagonism)
Question » if they move from their site of synthesis (and not all do), may diffuse from cell to cell,
be actively transported or be carried in the phloem or xylem
10 What is the » may have profoundly differing effects, depending on whether they are present at a low
difference between
or high concentration
growth and
» may have different effects according which tissue they are in or at different stages of
development?
development of a single tissue.
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Auxins, principally indoleacetic acid (IAA)
Discovery
Initially by Darwin, investigating coleoptiles and their curvature towards a
indoleacetic acid (the principal auxin)
H
15
unilateral light source C
HC C C CH2 COOH
Later by others, including the devising of a biological assay to find
the concentrations of auxins in plant organs (since these are at low HC C CH
concentrations) C N
H H
Roles
» Promotion of extension growth of stems and roots (at different

concentrations)
» Dominance of terminal buds
» Promotion of fruit growth
» Inhibition of leaf fall
Synthesis
At stem and root tips and in young leaves (from the amino acid tryptophan)
Gibberellins (GAs)
Discovery gibberellins
e.g. gibberellic acid
Initially, in dwarf rice plants, which, when infected with a fungus O
(Gibberella sp.), responded by growing to full height 4
3
Roles C=O 7 OH
HO
» Promotion of extension growth of stems 8 CH2
» Delay of leaf senescence and leaf fall CH3
COOH
» Inhibition of lateral root initiation
» Switching on of genes to promote germination
Synthesis
In the embryos of seeds and in young leaves (except in genetically dwarf
varieties)
There are several types of gibberellin
Abscisic acid (ABA)
Discovery abscisic acid CH3
During investigation of bud and seed dormancy and in abscission of fruits H3C CH3
Roles H
» A stress hormone OH
» Triggering of stomatal closure when leaf cells are short of water COOH
O CH3
» Induction of bud and seed dormancy
Synthesis
In most organs of mature plants, in tiny amounts
▲ Table 15.2 The plant regulators: discovery, roles and synthesis. The structural formulae show how chemically diverse
these substances are – they do not require memorising.
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EXTENSION
15 Interactions of plant growth regulators terminal
bud
Sometimes plant growth regulators have their IAA produced here – inhibits
effects acting on their own, but in other situations, development of lateral buds below
they interact with other growth regulators. stem cytokinin also produced here –
opposes effects of IAA, promoting
When one substance enhances the effect of the development of lateral buds =
other, this is known as synergism. For example, antagonism
gibberellins (GAs) and indoleacetic acid (IAA)
GA + IAA interact to reinforce the

work synergistically in stem extension growth effect of each other, enhancing
(Figure 15.19). extension growth of the stem in
the internodes = synergism
Alternatively, a growth regulator may reduce
lateral bud
the effect of another. This situation is known as internode
antagonism. Some important interactions involve leaf stalk
the other growth regulators (cytokinins – their
main role is in cell differentiation, and ethylene –
its main role is in fruit ripening).
leaf blade
node =
point of
attachment
of leaf
▲ Figure 15.19 The interaction of growth regulators
The Venus fly trap

The Venus fly trap (Dionaea muscipula) is a carnivorous plant, native to the subtropical
wetlands of the East Coast of the USA.
Remember, plants typically obtain the ions they need for their metabolism by active uptake
from the soil solution. However, in some habitats, the decay of dead organisms (by which
the ions are released into the soil solution) may be very slow, and when they are released,
the ions tend to be washed away by the high rainfall. In these environments carnivorous
plants that can trap minibeasts, such as flying insects, prosper. They take their essential
ions from the decaying or digested bodies of these victims, thus enabling
the plants to survive in these unfavourable growing conditions where
other plants often fail. The Venus fly trap is an example of this.
Look at Figure 15.20 now.
The margins of the leaves of this plant have short, stiff hairs, which
when they are bent by an insect large enough to do so, trigger the
two halves of the leaf to snap shut, trapping the insect. Then, short,
glandular hairs on the inner leaf surface secrete hydrolytic protease
enzymes that digest the soft tissue of the insect. Active uptake of the
ions released then takes place into the leaf cells. Later, the trap reopens
and the undigested matter is blown away.
The rapid closure of the Venus flytrap is one of the fastest movements
observed in the plant kingdom. It occurs in the complete absence of
a nervous system. It is due, at least in part, to an extremely sudden
change in turgidity of cells in the hinge region of the leaf blade.
However, how this rapid loss in turgor is brought about is not clear.
▲ Figure 15.20 Venus fly trap, with close-up Another hypothesis is a sudden acid-induced wall loosening in ‘motor
view of leaves, one closed with a trapped fly cells’ of the leaf – implying that proton pumps are involved.
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How auxin stimulates elongation growth
We have seen that auxin has a major role in the growth of the shoot apex, where it
promotes the elongation of cells. Auxin has this effect on growth and development by 15
direct action on the components of growing cells, including the walls. For example
auxin-triggered cell elongation occurs due to the stimulating effect of auxin on
proton pumps in the cell surface membranes of cells that lie beside the cellulose walls
(Figure 15.21). The result is that the walls become acidic, and the lowered pH initiates
the breakage of cross-links between cellulose microfibrils and binding polysaccharides
that had helped to make the cellulose inflexible. The wall’s resistance to stretching due

to turgor pressure is decreased and elongation occurs.
Note that auxin transport across cells is polar, with its entry into the cell being
passive (by diffusion), but its efflux is active (ATP-driven). Auxin efflux pumps set up
concentration gradients in plant tissues, in fact.
apex of stem/root
entry of auxin
by diffusion passive
auxin-influx
auxin channels cell wall (cellulose microfibrils
bound by other polysaccharides)
polar auxin transport

(passive entry above, active
pumping out at base of cell
by auxin efflux pumps) auxin-triggered cell
cytosol (with ribosomes,
elongation (acid growth
RER, SER, mitochondria auxin hypothesis)
and Golgi apparatus)
• auxin stimulates proton
pumps
plasma • wall becomes acidic
membrane • low pH triggers breakage of
vacuole cross-links between
cellulose microfibril and
binding polysaccharides
nucleus • hydrolytic enzymes attack
auxin exposed binding
polysaccharides
genes for growth/ • wall resistance to stretching
development is decreased – turgor of
auxin-mediated regulation
transcribed or cell causes stretching/
of gene expression
suppressed elongation of cell wall
(promotion/inhibition of
gene expression via
transcription regulation/ auxin
transcription factors)
base of stem/root ATP-activated

auxin efflux pumps
auxin pumped out
of cell here
▲ Figure 15.21 Auxin, proton pumps and cell elongation
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The role of gibberellin in the germination of barley
15 Many higher plants have been found to contain gibberellic acid (GA). In fact, several
different forms of the molecule have been discovered and these are often referred to
collectively as gibberellins. Gibberellins are formed in chloroplasts, in the embryo of
seeds and in young leaves. Gibberellins are absent from dwarf varieties of pea plants, but
when artificially supplied to dwarf varieties, they become tall.
The highest concentrations of gibberellins occur in fruits and seeds as they are formed
and in seeds as they germinate. In the seed, gibberellins switch on genes that promote
germination and go on to promote additional mitosis, thereby increasing the numbers
of cells formed. Gibberellins also have a role in the mobilisation of stored food in
germinating barley fruits, as illustrated in Figure 15.22, on the next page. During
germination, the uptake of water activates the gene for gibberellic acid synthesis. This
gibberellic acid then switches on the genes that control the synthesis of hydrolytic
enzymes. Hydrolytic enzymes catalyse the mobilisation of the food reserves, causing the
release of sugars, amino acids and fatty acids for germination and growth.
4 soluble food store translocated to embryo where

it is respired or used to build new cells (sugars are
translocated to the growing point as sucrose)
fruit and seed coat

3 gibberellic acid triggers synthesis
fused together
of hydrolytic enzymes
cells containing stored e.g. amylase (starch maltose)
protein (aleurone grains) maltase (maltose glucose)
site of starch store 2 gibberellic acid diffuses to

(endosperm) protein store
1 gibberellic acid formed in

embryo as germination begins
coleoptile
embryo and
cotyledon
uptake of water
leads to mobilisation of
stored food reserves
dormant
seed seedling grows at
expense of stored
food
▲ Figure 15.22 The role of gibberellic acid in the germination of barley fruit
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SUMMARY
» Hormones work with the animal’s nervous here is chemical, involving diffusion of a specific
15
system in the control and coordination of the body. transmitter substance.
Hormones are produced in endocrine glands, » Receptors contain sensory cells or dendrites of
transported all over the body in the blood and sensory neurones that respond to stimuli with
affect specific target organs. the production of action potentials. The brain
» The nervous system contains receptors (e.g. sense receives and integrates incoming information from
organs) linked to effectors (muscles or glands) by sensory receptors, sends impulses to effectors,

neurones, known collectively as reflex arcs. In stores information as a memory bank, and initiates
mammals, reflex arcs are coordinated in the spinal activities in its own right.
cord and may be connected to the brain. Neurones » Plant sensitivity and coordination is mediated by
are the basic units of the nervous system. The growth regulators (including auxins, gibberellins
nerve fibres of neurones, the dendron and axon, and abscisic acid) which are different from animal
are typically protected by a myelin sheath, which hormones.
also speeds conduction of the impulse. » Plant responses are mainly growth responses.
» An impulse or action potential is a temporary For example, the tips of plant stems grow
reversal of the electrical potential difference that towards the light, and plant stems and root tips
is maintained across the membrane of the nerve respond to gravity so the aerial shoot grows
fibres. Conduction is extremely fast and, after an up and the roots down. Auxins (principally
action potential, there is a brief period when the indoleacetic acid) maintain apical dominance of
fibre is not excitable (refractory period). Action stem; gibberellins are active in stem elongation
potentials are transmitted between neurones and in germination, and abscisic acid is involved
across tiny gaps at synapses. Transmission in the closure of stomata.

1 a Outline the roles of sensory receptor cells in the mammalian nervous
system. [3]
b Fig. 1.1 shows the changes in potential difference (p.d.) across the membrane
of a receptor cell over a period of time. The membrane was stimulated at
time A and at time B with stimuli of different intensities.
+60
+40
+20
membrane potential/mV
C D
–20
–40
threshold potential
–60
E
–80
0 1 2 3 4 5
time / ms
stimulus stimulus
A B
▲ Fig. 1.1
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i State which of the letters C, D and E on Fig. 1.1 correspond to each of these
events. You may use each of the letters C, D or E once, more than once or
15 not at all.
The Na+ / K+ pump is operating
The voltage‑gated Na+ channels are open
The voltage‑gated K+ channels are open [3]
ii Explain why stimulus A did not result in an action potential being
produced whereas stimulus B did. [2]
iii Describe the importance of the refractory period in the transmission of
[2]
action potentials.
iv Describe how action potentials are transmitted along a myelinated axon. [4]
[Total: 14]
2 a Outline the ways in which the endocrine and nervous systems carry out their
roles in control and coordination in animals. [8]
b Describe the part played by auxins in apical dominance in a plant shoot. [7]
[Total: 15]
(Cambridge International AS and A Level Biology 9700 Paper 41 Q9 June 2011)
3 One example of chemical control and coordination in plants is in the breakdown
of food reserves during the germination of cereal grains, such as wheat.
a Fig. 3.1 is a diagram of a grain of wheat.
The numbered arrows indicate the sequence of events that occurs after the
uptake of water by the grain of wheat.
A
2
▲ Fig. 3.1
i Name structures A, B and C, shown in Fig. 3.1. [3]

ii With reference to the three numbered arrows in Fig. 3.1, describe the
sequence of events that follows the uptake of water by the grain of wheat.[6]
[Total: 9]
4 a By means of a labelled diagram show the structure of a synapse. [5]
b Describe the sequence of steps by which an action potential crosses a
cholinergic synapse. [10]
c Outline the roles synapses play in the functioning nervous system. [5]
[Total: 20]
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A LEVEL
16 Inheritance
16.1 Passage of information from parents to offspring

Genetic information is Learning outcomes
transmitted from generation
to generation to maintain By the end of this topic, you will be able to:
the continuity of life. In 16.1.1 explain the meanings of the terms haploid (n) and diploid (2n)
sexual reproduction, meiosis 16.1.2 explain what is meant by homologous pairs of chromosomes
introduces genetic variation 16.1.3 explain the need for a reduction division during meiosis in the production
so that offspring resemble
of gametes
their parents but are not
identical to them. Genetic 16.1.4 describe the behaviour of chromosomes in plant and animal cells during
crosses reveal how some meiosis and the associated behaviour of the nuclear envelope, the
features are inherited. The cell surface membrane and the spindle (names of the main stages of
phenotype of organisms meiosis, but not the sub-divisions of prophase I, are expected: prophase I,
is determined partly by metaphase I, anaphase I, telophase I, prophase II, metaphase II,
the genes that they have anaphase II and telophase II)
inherited and partly by the 16.1.5 interpret photomicrographs and diagrams of cells in different stages of
effect of the environment. meiosis and identify the main stages of meiosis
Genes determine how
organisms develop; gene 16.1.6 explain that crossing over and random orientation (independent
control in bacteria gives us assortment) of pairs of homologous chromosomes and sister chromatids
a glimpse of this process in during meiosis produces genetically different gametes
action. 16.1.7 explain that the random fusion of gametes at fertilisation produces
genetically different individuals
Starting points
★ Diploid organisms contain pairs of homologous chromosomes.
★ The behaviour of maternal and paternal chromosomes during meiosis
generates much variation amongst individuals of the next generation.

Diploid organisms contain homologous pairs of chromosomes
We introduced the structure and features of chromosomes in Topic 5:
» The number of chromosomes per species is fixed.
» The shape of a chromosome is characteristic; they are of fixed length and with a
narrow region, called the centromere, somewhere along their length.
» The centromere is always in the same position on any given chromosome, and
this position and the length of the chromosome is how it can be identified in
photomicrographs.
» Chromosomes hold the hereditary factors, genes. A particular gene always occurs on
the same chromosome in the same position.
» The position of a gene is called a locus.
» Each gene has two or more forms, called alleles.
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The loci are the positions along the chromosomes
We have also seen that the nuclear division
that occurs during growth, known as mitosis,
16
where genes occur, so alleles of the same gene
occupy the same locus. results in the exact duplication of these
chromosomes in the daughter nuclei formed.
Examination of the chromosomes at certain
gene – a specific length of the DNA of the chromosome – a linear
chromosome, occupying a position called a sequence of many genes, some of
stages in mitosis discloses another important
locus A a which are shown here feature. Chromosomes occur in pairs.
alleles of a gene (allele is the short form
These pairs of chromosomes are known
of ‘allelomorph’ meaning ‘alternative as homologous pairs (Figure 16.1). These
form’)
homologous pairs of chromosomes arise in the
16 Inheritance
C C
first place because one member of the pair has
come from the male parent and the other from
the female parent. Homologous pairs are then
centromeres maintained by the exact replication that takes
place prior to each mitotic division. A cell with
a full set of chromosomes (two copies of each
F F
homologous chromosome), shown as 2n, in its
at these loci the genes are
homozygous (same alleles)
nucleus is said to be in the diploid condition.
j j loci
Meiosis – the reductive division
at this locus the gene is heterozygous M m There is a different type of nuclear division
(different alleles) that results in daughter nuclei each
containing half the number of chromosomes
of the parent cell.
chromosomes exist in pairs
– one of each pair came originally
In sexual reproduction, two sex cells (called
from each parent organism
gametes) fuse; this is fertilisation. The
▲ Figure 16.1 The genes and alleles of a homologous pair of chromosomes resulting cell is called the zygote, and it will
This is an animal life cycle. grow and develop into a new individual.
adult
Because two nuclei fuse when sexual reproduction occurs, the
2n chromosome number is doubled at that time. For example, human
meiosis gametes (each egg cell and sperm) have just 23 chromosomes each.
When the male and female gametes fuse, the full component of
46 chromosomes is restored.
diploid sperm egg haploid
phase n n phase The doubling of the number chromosome each time sexual
reproduction occurs (every generation) is avoided by a nuclear division
fertilisation
that halves the chromosome number. This reductive division is called
zygote
meiosis. The sex cells formed following meiosis contain only one
mitosis 2n of each homologous pair of chromosomes, shown as n, a condition
known as haploid. When haploid gametes fuse the resulting cell has
Self-fertilisation = sperm + egg from same individual. the diploid condition again.
Cross-fertilisation = sperm + egg from different individuals. The differences between mitosis and meiosis are summarised in
▲ Figure 16.2 Meiosis and the diploid life cycle Figure 5.4, page 111.
EXTENSION
Asexual reproduction
Organisms reproduce asexually or sexually and many reproduce by both these
methods. In asexual reproduction a single organism produces new individuals.
Asexual means ‘non-sexual’; no gametes are formed in asexual reproduction. The
cells of the new offspring are produced by mitosis (page 111), so the progeny are
identical to the parent and to each other. Identical offspring produced by asexual
reproduction are known as clones.
Mammals reproduce by sexual reproduction only, but many flowering plants
reproduce by both asexual and sexual reproduction.
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The process of meiosis
Once started, meiosis proceeds steadily as a continuous process of nuclear division.
However, the steps of meiosis are explained in four distinct phases (prophase, 16
metaphase, anaphase and telophase). This is just for convenience of analysis and
Question description, there are no breaks between the phases in nuclear divisions.
1 a Explain why The behaviour of the chromosomes in the phases of meiosis is shown in Figure 16.4, overleaf.
chromosomes For clarity, the drawings show a cell with a single pair of homologous chromosomes.
occur in
homologous pairs Meiosis involves two divisions of the nucleus, known as meiosis I and meiosis II.

in diploid cells. Both of these divisions superficially resemble mitosis. For example, as happens in mitosis,
chromosomes are copied, appearing as sister chromatids during interphase, before
b How do the
meiosis occurs. However, early in meiosis I, homologous chromosomes pair up. By the
products of
end of meiosis I, homologous chromosomes have separated again, but the chromatids
mitosis and
meiosis differ? they consist of do not separate until meiosis II. So, meiosis consists of two nuclear
divisions but only one replication of the chromosomes.
Meiosis I
Prophase I
What happens to chromosomes during prophase I is quite complex and difficult to see
when you are looking at dividing cells under the microscope. However, you can follow the
changes in Figure 16.4.
The chromosomes appear under the light microscope as single threads with many tiny
bead-like thickenings along their lengths. These thickenings represent an early stage in
the process of shortening and thickening by coiling that continues throughout prophase.
In fact, each chromosome has already replicated and consists of two chromatids but the
individual chromatids are not visible as yet.
The formation of pairs of homologous chromosomes

As the chromosomes continue to thicken, homologous chromosomes are seen to come
together in specific pairs, point by point, all along their length. Remember, in a diploid
cell each chromosome has a partner that is the same length and shape and with the
same linear sequence of genes.
The homologous chromosomes continue to shorten and thicken. Later in prophase the
individual chromosomes can be seen to be double-stranded, as the sister chromatids
become visible.
Crossing over
Within the homologous pair, during the coiling and shortening process, breakages of
the chromatids occur frequently. Breakages occur in non-sister chromatids at the same
points along the length of each. Broken ends rejoin more or less immediately, but where
the rejoining is between non-sister chromatids, swapping
of pieces of the chromatids has occurred, hence the name
‘crossing over’. This results in new combinations of genes on
the chromosomes.
The point of the join between different chromatids is called
a chiasma (plural: chiasmata). Virtually every pair of
homologous chromosomes forms at least one chiasma at this
time, and two or more chiasmata in the same homologous
pair is very common (Figure 16.3).
In the later stage of prophase I the attraction and tight pairing of
▲ Figure 16.3 Photomicrograph of homologous the homologous chromosomes ends, but the attractions between
chromosomes held together by chiasmata sister chromatids remains for the moment (Figure 16.5, overleaf).
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This attraction of sister chromatids keeps the homologous pairs together. The chromatids
are now at their shortest and thickest.
16 In late prophase I the two centrioles of the centrosome present in animal cells (page 19)
duplicate. The two centromeres then start to move apart as a prelude to spindle formation.
Plant cells do not have centrioles.
Finally, the disappearance of the nucleoli and nuclear envelope marks the end of
prophase I.
16 Inheritance
MEIOSIS I
prophase I (early) prophase I (mid)
During interphase the chromosomes Homologous chromosomes pair
replicate into chromatids held together up as they continue to shorten
by a centromere (the chromatids are and thicken. Centrioles duplicate.
not visible). Now the chromosomes
condense (shorten and thicken) and
become visible.
prophase I (late) metaphase I

Homologous chromosomes repel each Nuclear envelope breaks down.
other. Chromosomes can now be seen Spindle forms. Homologous pairs
to consist of chromatids. Sites where line up at the equator, attached
chromatids have broken and rejoined, by centromeres.
causing crossing over, are visible as
chiasmata.
anaphase I telophase I
Homologous chromosomes separate Nuclear envelope re-forms around
and whole chromosomes are pulled the daughter nuclei. The
towards opposite poles of the spindle, chromosome number has been
centromere first. halved. The chromosomes start
to decondense.
there is no interphase between MEIOSIS I and MEIOSIS II
prophase II MEIOSIS II metaphase II

The chromosomes condense and the The nuclear envelope breaks
centrioles duplicate. down and the spindle forms. The
chromosomes attach by their
centromere to spindle fibres at
the equator of the spindle.
anaphase II telophase II
The chromatids separate at their The chromatids (now called
centromeres and move to chromosomes) decondense.
opposite poles of the spindle. The nuclear envelope re-forms.
The cytoplasm divides.
▲ Figure 16.4 The process of meiosis
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1 Homologous chromosomes 3 Rejoining of non-sister chromatids 5 Once pairs of homologous
commence pairing as they forms chiasmata. This results in new chromosomes have separated,
16
continue to shorten and thicken combinations of genes on the sites of crossing over
by coiling. the chromosomes. are not apparent.

4 Positions of chiasmata become visible
2 Breakages occur in parallel non-sister
later, as tight pairing of homologous
chromatids at identical points.
chromosomes ends. The chiasmata
indicate where crossing over has
occurred.
▲ Figure 16.5 The formation of chiasmata
Metaphase I
Next, the spindle forms, and the homologous pairs become attached to individual
microtubules of the spindle by their centromeres. The homologous pairs are now
arranged at the equatorial plate of the spindle framework – we say that they line up at the
centre of the cell. By the end of metaphase I, the members of the homologous pairs start
to repel each other and separate. However, at this point they are held together by one or
more chiasmata and this gives a temporary but unusual shape to the homologous pair.
Anaphase I
The chromosomes of each homologous pair now move to opposite poles of the spindle,
but with the individual chromatids remaining attached by their centromeres. The
attraction of sister chromatids has lapsed, and they separate slightly – both are clearly
visible. However, they do not separate yet; they go to the same pole. Consequently,
meiosis I separates homologous pairs of chromosomes but not the sister chromatids of
which each is composed.
Telophase I
The arrival of homologous chromosomes at opposite poles signals the end of meiosis
I. The chromosomes tend to uncoil to some extent, and a nuclear envelope re-forms
around both nuclei. The spindle breaks down, but these two cells do not go into
interphase, rather they continue into meiosis II, which takes place at right angles to
meiosis I. There may, however, be a delay between meiosis I and meiosis II.
Questions 2 What is the major consequence of there being no interphase between meiosis I and
meiosis II?
3 At precisely which points in the process of meiosis (Figure 16.4) do the following events
occur?
a the nuclear envelope breaks down and the spindle forms
b homologous chromosomes pair up
c the presence of chiasmata becomes visible
d chromatids separate at their centromeres
e homologous chromosomes separate
f haploid nuclei form
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Meiosis II
16 Meiosis II is remarkably similar to mitosis:
» Prophase II
The nuclear envelopes break down again, and the chromosomes shorten and re-
thicken by coiling. Centrioles, if present, duplicate and move to opposite poles of
the cell. By the end of prophase II the spindle apparatus has re-formed, but at right
angles to the original spindle.
» Metaphase II
The chromosomes line up at the equator of the spindle, attached by their centromeres.
16 Inheritance
» Anaphase II
The centromeres divide and the chromatids move to opposite poles of the spindle,
centromeres first.
» Telophase II
Nuclear envelopes form around the four groups of chromatids, so that four nuclei
are formed. Now there are four cells, each with half the chromosome number of
the original parent cell. Finally, the chromatids – now recognised as chromosomes,
uncoil and become apparently dispersed as chromatin. Nucleoli re-form.
The process of meiosis is now complete, and is followed by division of the cytoplasm
(cytokinesis, page 110).
Meiosis and genetic variation

There are differences in the genetic information carried by different gametes. This
variation arises in meiosis and is highly significant for the organism, as we shall see. The
reason why the four haploid cells produced by meiosis differ genetically from each other
is because of two important features of meiosis. These are:
» the independent assortment of maternal and paternal homologous
chromosomes. The way the chromosomes of each homologous pair line up at the
equator of the spindle in meiosis I is entirely random. Which chromosome of a
given pair goes to which pole is unaffected by (independent of) the behaviour of
the chromosomes in other pairs. Figure 16.6 shows a parent cell with only four
chromosomes, for clarity. Of course, the more homologous pairs there are in the
nucleus, the greater the variation that is possible. In humans there are 23 pairs of
chromosomes, so the number of possible combinations of chromosomes that can be
formed as a result of independent assortment is 223. This is over 8 million.
» the crossing over of segments of individual maternal and paternal homologous
chromosomes. This results in new combinations of genes on the chromosomes of
the haploid cells produced, as illustrated in Figure 16.7. Crossing over generates the
possibility of an almost unimaginable degree of variation. For example, if we were to
assume for sake of discussion that there are 30 000 individual genes on the human
chromosome complement, all with at least two alternative alleles, and that crossing
over is equally likely between all of these genes, then there are 230 000 different
combinations! Of course, all these assumptions will be inaccurate to varying extents,
but the point that virtually unlimited recombinations are possible is established.
Finally, further genetic variation in the progeny of organisms that reproduce sexually is
assured by the random fusion of male and female gametes in sexual reproduction.
A note on ‘recombinants’
Question Offspring with combinations of characteristics different from those of their parents
are called recombinants. Recombination in genetics is the re-assortment of alleles or
4 What are the characters into different combinations from those of the parents. We have seen that
essential differences
recombination occurs for genes located on separate chromosomes (unlinked genes)
between mitosis and
by chromosome assortment in meiosis (Figure 16.6), and for genes on the same
meiosis?
chromosomes (linked genes) by crossing over during meiosis (Figure 16.7).
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We shall see in the next section, how crossing over, random assortment of homologous
chromosomes during meiosis, and random fusion of gametes at fertilisation may also
lead to the expression of rare, recessive alleles, such as those that are responsible for
albinism, sickle cell anaemia, haemophilia and Huntington’s disease.
16
nucleus of parent cell Independent assortment is illustrated
(diploid) in a parent cell with two pairs of
homologous homologous
chromosomes chromosomes homologous chromosomes. The
more pairs of homologous
chromosomes there are, the
greater the variation that is possible.

A a b B In humans, for example, there are
In meiosis I the pairs of homologous 23 pairs of chromosomes giving over
chromosomes move to the equator 8 million combinations.
of the spindle and line up randomly.
Then, when homologous chromosomes
separate they move to the nearest pole.
This may occur… …like this… or …like this
A a A a
B b b B
In meiosis II the final
outcome is one of these,
alternative combinations
of four haploid cells.
or
A B a b A B a b A b a B A b a B
Here the resulting gametes Here the resulting gametes

will be 1/2 AB, 1/2 ab. will be 1/2 Ab,1/2 aB.
▲ Figure 16.6 Genetic variation due to independent assortment
centromere
The effects of genetic variation
are shown in one pair of Homologous A B C chromatids
homologous chromosomes. chromosomes paired.
Typically, two, three or more A B C
chiasmata form between the a b c
chromatids of each homologous
pair at prophase I. a b c
chiasma chiasma
When the chromatids break
A B C
at corresponding points
along their length, their A B C
rejoining may cause a b c
crossing over.
a b c
A B C parental
combination
The chromatids finally
separate and move to a B c
haploid nuclei in meiosis II,
producing new genetic
combinations. A b c new genetic
combinations
a b C
▲ Figure 16.7 Genetic variation due to crossing over between non-sister chromatids
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16.2 The roles of genes in determining the phenotype
16.2.1 explain the terms gene, locus, allele, dominant, recessive, codominant,
linkage, test cross, F1, F2, phenotype, genotype, homozygous and
heterozygous
16.2.2 interpret and construct genetic diagrams, including Punnett squares, to
explain and predict the results of monohybrid crosses and dihybrid crosses
16 Inheritance
that involve dominance, codominance, multiple alleles and sex linkage

explain and predict the results of dihybrid crosses that involve autosomal
linkage and epistasis (knowledge of the expected ratios for different types
of epistasis is not expected)
explain and predict the results of test crosses
16.2.5 use the chi-squared test to test the significance of differences between
observed and expected results (the formula for the chi-squared test will
be provided, as shown in the Mathematical requirements)
Starting point
★ Patterns of inheritance are explained by using genetic diagrams. The results
of genetic crosses are analysed statistically using the chi-squared test.
Inheriting genes in sexual reproduction

In sexual reproduction haploid gametes are formed by meiosis. At fertilisation, male and
female gametes fuse to form a zygote. As a consequence, the zygote, a diploid cell, has
two sets of chromosomes (homologous pairs), one from each parent. Thus there are two
alleles of each gene present in the new individual.
Genotype and phenotype

The alleles that an organism carries (present in every cell) make up the genotype of that
organism. A genotype in which the two alleles of a gene are the same is said to ‘breed
true’ or to be homozygous for that gene. In Figure 16.11 (overleaf), the parent pea plants
(P generation) were either homozygous tall or homozygous dwarf. Alternatively, if the
alleles are different the organism is heterozygous for that gene. In Figure 16.11, the F1
generation were all heterozygous tall.
So the genotype is the genetic constitution of an organism. Alleles interact in various
ways (and with environmental factors, as we shall see later). The outcome is the
phenotype. The phenotype is the way in which the genotype of the organism is
expressed. It is the appearance of the organism. Here the dwarfness and tallness of the
plants were the phenotypes observed.
The monohybrid cross

The mechanism of inheritance was successfully investigated before chromosomes had
been observed or genes were known about. It was Gregor Mendel who made the first
important discoveries about heredity (Figure 16.8).
An investigation of the inheritance of a single contrasting characteristic is known as
a monohybrid cross. It had been noticed that the garden pea plant was either tall or
dwarf. How this contrasting characteristic is controlled is made clear by analysing the
monohybrid cross.
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In Figure 16.10 overleaf the steps of this investigation into the inheritance of height in
the pea plants is summarised. Note that the experiment began with plants that always
bred true, that is the tall plants produced progeny that were all tall and the dwarf
plants produced progeny that were all dwarf, when each was allowed to self-fertilise.
16
Self-fertilisation is the normal condition in the garden pea plant.
EXTENSION
Gregor Mendel – the founder of modern genetics

Gregor Mendel was born in eastern Europe in 1822,
the son of a peasant farmer. As a young boy he
worked to support himself through schooling, but at
the age of 21 he was offered a place in the monastery
at Bruno (now in the Czech Republic). The monastery
was a centre of research in natural sciences and
agriculture, as well as in the humanities. Mendel was
successful there. Later, he became Abbot.
Mendel discovered the principles of heredity by
studying the inheritance of seven contrasting
characteristics of the garden pea plant. These did not
‘blend’ on crossing, but retained their identities, and
were inherited in fixed mathematical ratios.
He concluded that hereditary factors (we now
call them genes) determine these characteristics, ▲ Figure 16.8 Gregor Mendel
that these factors occur in duplicate in parents, and that the two copies of the
factors segregate from each other in the formation of gametes.
Today we often refer to Mendel’s laws of heredity, but Mendel’s results
were not presented as laws – which may help to explain the difficulty
others had in seeing the significance of his work at the time.
Mendel was successful because:
l his experiments were carefully planned, and used large samples
l he carefully recorded the numbers of plants of each type but
expressed his results as ratios
l in the pea, contrasting characteristics are easily recognised (Figure 16.9)
l by chance, each of these characteristics was controlled by a
single factor (gene)* rather than by many genes, as most
human characteristics are
l pairs of contrasting characters that he worked on were
controlled by factors (genes) on separate
chromosomes*
l in interpreting results, Mendel made use
of the mathematics he had learnt.
* Genes and chromosomes were not known then.
Question
round v. wrinkled seeds
5 At the time of
Mendel’s experiments
it was thought that
the characteristics of
parents ‘blended’ in green v. yellow
their offspring. What cotyledons
(seed leaves)
features of Mendel’s
methods enabled him dwarf v. tall plants
to avoid this error? ▲ Figure 16.9 Features of the garden pea
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peas from peas from
pure-breeding tall plants pure-breeding dwarf plants
16
sown and grown (about 10–15 plants of each)
parental tall plants dwarf plants

generation (P)
crossed
×
16 Inheritance
self-fertilisation
was prevented
at this stage
many seeds produced

first filial (150–250 seeds typically harvested) –
generation (F1) planted and grown, and found to be
all tall plants
flowered and allowed to

self-fertilise
seeds produced
(Mendel recorded 1064 seeds) –
second filial planted and grown, and found
generation (F2) to be in the ratio of
3 tall : 1 dwarf plants
(Mendel recorded 787 tall : 277 dwarf, a ratio of 2.84 : 1)
▲ Figure 16.10 The steps of the monohybrid cross
In the monohybrid cross it appears that the ‘dwarf’ characteristic disappeared in the
first generation (F1 generation) but then reappeared in the F2 generation. We can explain
what is going on if there is a factor controlling ‘dwarfness’. This ‘factor’ remained intact
from one generation to another. However, it does not have any effect (we say it does
not ‘express itself’) in the presence of a similar factor for ‘tall’. In other words, ‘tall’ is a
dominant characteristic and ‘dwarf’ is a recessive characteristic. So there must be two
independent factors for height, one from one parent and the other factor from the other
parent. A sex cell (gamete) must contain only one of these factors.
Today we see that these ‘factors’ are alleles of the gene for height in the pea plant. When
the tall plants of the F1 generation were allowed to self-fertilise, the resulting members
of the F2 generation were in the ratio of 3 tall plants to 1 dwarf plant (Figure 16.10). The
genetic diagram in Figure 16.11 is the way we explain what is going on.
From the monohybrid cross we see that:
» within an organism are genes (called ‘factors’ when first discovered) controlling
characteristics such as ‘tall’ and ‘dwarf’
» there are two alleles of the gene in each cell
» one allele has come from each parent
» each allele has an equal chance of being passed on to an offspring
» the allele for tall is an alternative form of the allele for dwarf
» the allele for tall is dominant over the allele for dwarf.
We call this the law of segregation.
During meiosis, pairs of alleles separate so that each cell has one allele of a pair.
Allele pairs separate independently during the formation of gametes.
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parental (P)
phenotypes: homozygous homozygous
tall dwarf pea plants are diploid
so they have two 16
genotypes: TT × tt copies of each allele
(meiosis) (meiosis)
gametes produced by
meiosis so only have
gametes: T t one copy of each allele
the allele for ‘tall’ is

dominant over the

allele for ‘dwarf’ so
offspring (F1) the F1 progeny are
all tall
genotypes: Tt
heterozygous tall each heterozygous
phenotypes: × self parent produces two
kinds of gametes with
respect to the T allele
segregation occurs
during meiosis –
F1 selfed
alleles are located
on homologous
chromosomes which
gametes: (meiosis) (meiosis) move to opposite
poles of the spindle
T t T t
alleles have
separated into
different gametes
(= law of segregation)
fe
es
m
et
al
1
T
1
m
e
2
ga
ga
T
2
m
1
e
TT
al
et
this is called a Punnett square –
m
es
4
homozygous it shows all the possible
tall plants progeny of the cross
1
t
1
2
2
1 1
Tt Tt
4 4
heterozygous heterozygous
here both and gametes
tall plants tall plants
can be T or t, giving four
1 possible genotypes
tt
The fractions represent 4
the probabilities that homozygous
particular gametes and dwarf plants
zygotes (genotypes)
will occur.
offspring (F2)
genotypes: TT Tt tt
genotypes ratio: 1 : 2 : 1
These ratios are likely to
be achieved only when
phenotypes: tall dwarf large numbers of offspring
are produced.
phenotypes ratio: 3 : 1
▲ Figure 16.11 Genetic diagram showing the behaviour of alleles in the monohybrid cross
Question 6 From the Punnett square in Figure 16.11, a ratio of 3 tall to 1 dwarf pea plants was
predicted. In fact, a ratio of 2.84 : 1 occurred (Figure 16.10). Suggest what chance
events may influence the actual ratios of offspring obtained in breeding experiments
like these.
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The test cross
16 If an organism shows a recessive characteristic in its phenotype (for example, it is

a dwarf pea plant) it must have a homozygous genotype (tt). However, if it shows
the dominant characteristic (for example, it is a tall pea plant) then it may be either
homozygous for the dominant allele (TT) or heterozygous for the dominant allele (Tt).
In other words, TT and Tt look alike. They have the same phenotype but different
genotypes.
You can tell plants like these apart only by the offspring they produce in a particular
cross. When tall heterozygous plants (Tt) are crossed with homozygous recessive plants
16 Inheritance
(tt), the cross yields 50 per cent tall and 50 per cent dwarf plants (Figure 16.12). This
type of cross has become known as a test cross. If the offspring produced were all tall
this would show that the tall parent plants were homozygous plants (TT). Of course,
sufficient plants have to be used to obtain these distinctive ratios.
parental
phenotypes: heterozygous homozygous
tall dwarf
genotypes: Tt × tt
(meiosis) (meiosis)
gametes: T t t t
ga
es
t
1
et
m
2
t
2
m
et
1
ga
es
tt
4
homozygous
dwarf plants
1
T
1
2
t
2
1 1
Tt tt
4 4
heterozygous homozygous
tall plants dwarf plants
The fractions represent
the probabilities that 1
Tt
particular gametes and 4
zygotes (genotypes) heterozygous
will occur. tall plants
offspring (F1)
genotypes: TT tt
genotypes ratio: 1 : 1
phenotypes: tall dwarf
phenotypes ratio: 50% : 50%
▲ Figure 16.12 Genetic diagram showing the behaviour of alleles in the monohybrid test cross
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Modification of the 3 : 1 ratio
In certain types of monohybrid cross the 3 : 1 ratio is not obtained. Two of these
situations are now illustrated. 16
Codominance – when both alleles are expressed
In the case of some genes, both alleles may be expressed, rather than one being
dominant and the other recessive in the phenotype, as has been the case up to now.
When both alleles are expressed codominantly we know that both are transcribed into
messenger RNA.

An example of codominance is the case of the haemoglobin b-polypeptide gene, where
the phenotype of a person who has the genotype HbA HbA is unaffected by sickle cell
disorder, the phenotype of a person who has the genotype HbA HbS is the less severe
sickle cell trait and the phenotype of a person who has the genotype HbS HbS is the
more severe sickle cell anaemia. You can see that, in a cross between parents both of
whom have the sickle cell trait, the probability that any offspring will have sickle cell
anaemia is one in four (Figure 16.13).
parental
person with person with
phenotypes: sickle cell trait sickle cell trait
genotypes: HbA HbS × HbA HbS
(meiosis) (meiosis)
Question HbA HbS HbA HbS
7 Construct for
1
yourself (using A
b 2 H
ga
es
H bA
pencil and paper) a
et
1
m
m
et
2
ga
es
monohybrid cross 1
HbA HbA
between cattle of a S 4
1
b
H
2
H
1
variety with a gene
b
S
2
for coat colour with 1
HbA HbS
1
HbA HbS
4 4
codominant alleles,
‘red’ and ‘white’ coat.
Homozygous parents 1
HbS HbS
4
produce ‘roan’
offspring (red and
white hairs together). offspring (F1)
Predict what genotypes: HbA HbA HbA HbS HbS HbS
offspring you
genotypes ratio: 1 : 2 : 1
expect and in
what proportions phenotypes: person with person with person with
when a sibling normal sickle cell trait sickle cell
cross (equivalent to haemoglobin anaemia
‘selfing’ in plants) phenotypes ratio: 25% 50% 25%
occurs between roan
offspring. ▲ Figure 16.13 Genetic diagram showing the inheritance of sickle cell haemoglobin – an
example of codominance
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More than two alleles exist for a particular locus
16 To begin this discussion we considered the inheritance of a gene for which there are
just two forms (two alleles), like the ‘height’ gene of the garden pea, which has tall and
dwarf alleles. We represented this situation in a genetic diagram using a single letter
(T or t) according to whether we were representing the dominant or the recessive allele.
However, we now know that not all genes are like this. In fact, most genes have more
than two alleles, and these are cases of multiple alleles.
With multiple alleles, we choose a single capital letter to represent the locus at which
the alleles may occur and represent the individual alleles by a single capital letter in a
16 Inheritance
superscript position (Table 16.1) – as with codominant alleles.

An excellent example of multiple alleles is those controlling the human ABO blood
group system. Each person’s blood belongs to one of either A, B, AB or O group. Table
16.1 lists the possible phenotypes and the genotypes that may be responsible for each.
So, the ABO blood group system is determined by various combinations of alternative
alleles. In each individual only two of these three alleles exist, but they are inherited
as if they were alternative alleles of a pair. Alleles IA and IB are dominant to IO which
is recessive. Alleles IA and IB are codominant alleles. Figure 16.14 shows one possible
cross between parents with different blood groups.
Phenotype Genotypes parental (P)

IO is recessive IO is recessive
A IA IA or IA IO phenotypes: blood group A to IA blood group B to IB
B IB IB or IB IO genotypes: IA IO IB IO
(meiosis) (meiosis)
AB IA IB
O IO IO
1 1 1 1
gametes: IA IO IB IO
▲ Table 16.1 The 2 2 2 2
ABO blood groups

– phenotypes and
IA and IB are codominant –
genotypes
they both affect the
phenotype when present
together in the heterozygote.
1
IA
1 2
ga
es
et
m
2
B
I
m
et
ga
es
1 A B
4
I I 1
IO
1 2
2
O
I
1 B O 1 A O
4
I I 4
I I
The fractions represent

the probabilities that
particular gametes and 1 O O
I I
zygotes (genotypes) 4
will occur.
IO IO gives blood
group O
offspring
genotypes: IA IB IA IO IB IO IO IO
genotypes ratio: 1 : 1 : 1 : 1
phenotypes: blood blood blood blood

group AB group A group B group O
phenotypes ratio: 25% 25% 25% 25%
▲ Figure 16.14 Genetic diagram showing the inheritance of human blood ABO group alleles
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Question Reviewing the genetic terms learnt so far
8 One busy night in
an understaffed
Table 16.2 lists the essential genetic terms and defines each, succinctly.
Cover the right hand column with a piece of paper, temporarily, and see if you can define each
16
maternity unit, four correctly, in your own words.
children were born
about the same time. Haploid a eukaryotic cell or organism containing only one complete set of
Then the babies chromosomes (only one of each homologous chromosome)
were muddled up by Diploid a eukaryotic cell or organism containing two complete sets of
mistake; it was not chromosomes (two copies of each homologous chromosome)

certain which child
Gene a length of DNA that codes for a particular polypeptide or protein
belonged to which
family. Fortunately Allele one of two or more alternative nucleotide sequences at a single gene
the children had locus; alleles are variant forms of genes
different blood Locus the position on the chromosome where a gene occurs; alleles of the same
groups: A, B, AB gene occupy the same locus
and O. Genotype the genetic constitution of an organism with respect to a gene or genes
The parents’ blood
Phenotype the physical, detectable expression of the particular alleles of a gene or
groups were also
genes present in an individual
known:
Homozygous a term describing a diploid organism that has the same allele of a gene at
» Mr and Mrs Jones
the gene’s locus on both copies of the homologous chromosomes in its cell
A and B
» Mr and Mrs Lee Heterozygous a term describing a diploid organism that has different alleles of a gene at
B and O the gene’s locus on both copies of the homologous chromosomes in its cell
» Mr and Mrs Dominant an allele that affects the phenotype of the organism whether present in
Gerber O and O allele the heterozygous or homozygous condition
» Mr and Mrs Recessive an allele that affects the phenotype of the organism only when the
Santiago AB allele dominant allele is absent (i.e. the individual is homozygous recessive)
and O Codominant alleles that are both expressed if they are present together in a
Staff were able to alleles heterozygous person
decide which child
Test cross testing a suspected heterozygote by crossing it with a known
belonged to which
homozygous recessive
family. How was this
done? ▲ Table 16.2 Essential genetic terms
Sex chromosomes
In humans, inheritance of sex is controlled by specific chromosomes known as the
sex chromosomes. Each of us has one pair of sex chromosomes (either XX or XY
chromosomes) along with the 22 other pairs. (These others are known as autosomal
chromosomes.)
Female gametes produced by meiosis all carry an X chromosome, but half of male
gametes carry an X chromosome and half carry a Y chromosome. At fertilisation, a
female gamete may fuse with a male gamete carrying an X chromosome, which results
in a female offspring. Alternatively, the female gamete may fuse with a male gamete
carrying a Y chromosome, which results in a male offspring.
So, the sex of offspring in humans (and all mammals) is decided by which type of male
gamete fuses with the female gamete – that is, by the male.
Note also that we would expect equal numbers of male and female offspring to be
produced by a breeding population over time.
How human X and Y chromosomes control sex

Both male and female embryos develop identically in the uterus, initially. At the seventh
week of pregnancy, however, if a Y chromosome is present in the embryonic cells a
cascade of developmental events is triggered, leading to the growth of male sex organs.
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parental (P)
16 phenotypes: human male ( ) human female ( )
genotypes: XY XX
(meiosis) (meiosis)
gametes: 1 X 1 Y 1 X 1 X
2 2 2 2
)
16 Inheritance
fe
(
m
es
1
al
X
et
e
1 2 X
ga
2
ga
m
e
et
al
1
es
m
XX 1
(
4
1 Y 2 X
)
2
1 1
XY XX
4 4
1
XY
4
offspring (F1)
genotypes: XY XX
Figure 16.15 X and Y phenotypes: male ( ) female ( )

▲
chromosomes and the

phenotypes ratio: 50% 50%
determination of sex
On the Y chromosome is the prime male-determining gene. This gene codes for a
protein – the testis determining factor (TDF). TDF functions as a molecular switch;
on reaching the embryonic gonad tissues, TDF initiates the production of a relatively
low level of testosterone. The effect of this hormone at this stage is to inhibit the
development of female sex organs and to cause the formation of the testes, scrotum and
penis. In the absence of a Y chromosome an ovary develops. Then, partly under the
influence of hormones from the ovary, the female reproductive structures develop.
Sex linkage
It is obvious that any gene present on the sex chromosomes is likely to be inherited with
the sex of the individual. These genes are said to determine sex-linked characteristics.
However, the inheritance of these sex-linked genes is different from the inheritance of genes
on the other chromosomes present. This is because the X chromosome is much longer
than the Y chromosome, so many of the genes on the X chromosome are absent from the Y
chromosome. In a male (XY), an allele present on the X chromosome is most likely to be on
its own and will be apparent in the phenotype even if it is a recessive allele.
Meanwhile, in a female, a single recessive gene is often masked by a dominant allele
on the other X chromosome, and in these cases the recessive allele is not expressed.
A human female can be homozygous or heterozygous with respect to sex-linked
characteristics, whereas males will have only one allele.
‘Carriers’
In a heterozygous individual with one dominant allele and one recessive allele of a gene,
the recessive allele will not have an effect on their phenotype. The individual is known
as a carrier. They ‘carry’ the allele but it is not expressed. It is masked by the presence
of the dominant allele.
Consequently, female carriers are heterozygous for sex-linked recessive characteristics.
In the case of a male (XY), the unpaired alleles of the X chromosome are all expressed.
The alleles on the short Y chromosome are mostly concerned with male structures and
male functions.
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However, there are some recessive genetically-inherited conditions caused by recessive
alleles on the X chromosome. Examples of these are Duchene muscular dystrophy, red–
green colour blindness and haemophilia. Notice that these examples are genetically-
inherited conditions.
16
The consequence of the presence of one of these alleles may be quite different for males
and females. This is because, if a single recessive allele is present in a male human, the
allele will be expressed. Meanwhile, a female must be homozygous recessive for a sex-
linked characteristic for the allele to be expressed. A female who is heterozygous for one
of these will be a ‘carrier’. We can illustrate this point by looking at the inheritance of

the conditions of red–green colour blindness and of haemophilia.
Red–green colour blindness

Question
A person who is red–green colour blind sees the colours green, yellow, orange and red all
9 a H
ow is the as the same colour. The condition affects about 8 per cent of males, but only 0.4 per cent of
genetic females in the human population. This is because a female may be homozygous, with both
constitution of alleles for normal development of cones in the retina (XB XB), or she may be heterozygous,
a female who is with an allele for normal colour vision and a mutant allele for abnormal development of
red–green these cones (XB Xb). For a female to be red–green colour blind, she must be homozygous
colour blind recessive for this allele (Xb Xb) and this occurs extremely rarely. On the other hand a male
represented? with a single recessive allele for red–green colour blindness (Xb Y) will be affected.
b Explain why it is
The inheritance of red–green colour blindness is illustrated in Figure 16.16. It is helpful
impossible to be a
for those who are red–green colour blind to recognise their inherited condition. Red–
‘carrier’ male.
green colour blindness is detected by the use of multicoloured test cards.
Colour blindness is detected by multicoloured

parental (P)
test cards. A mosaic of dots is arranged on the
cards so that those with normal colour vision phenotypes: carrier female ( ) normal male ( )
see a pattern that is not visible to those with
colour blindness. B
X X b B
X Y
genotypes: (meiosis) (meiosis)
gametes: 1 XB 1 Xb 1 XB 1 Y
2 2 2 2
)
m
(
1
al
es
b
e
2
et
X XB
ga
1
m
m
ga
2
et
e
es
al
1
XB Xb
m
B 1
fe
4
1 X
)
2 Y
2
1 1
XB XB Xb Y
4 4
1
XB Y
4
offspring (F1)
genotypes: XB XB XB Xb XB Y Xb Y
phenotypes: normal carrier normal colour blind

colour vision colour vision
females males
( ) ( )
phenotypes ratio: 25% : 25% : 25% : 25%
▲ Figure 16.16 The detection and inheritance of red-green colour blindness
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The dihybrid cross
16 Another early investigation by Mendel into the inheritance of variation involved two
pairs of contrasting characters, again using the garden pea plant. This is now referred
to as a dihybrid cross.
For example, pure-breeding pea plants from round seeds with yellow cotyledons
(seed leaves) were crossed with pure-breeding plants from wrinkled seeds with green
cotyledons (P generation). All the progeny (F1 generation) had round seeds with yellow
cotyledons.
16 Inheritance
When plants grown from these seeds were allowed to self-fertilise the following season,
the resulting seeds (F2 generation) – of which there were more than 500 to be classified
and counted – were of four phenotypes and were present in the ratio shown in Table
16.3 and in Figure 16.17.
Phenotype round seed / round seed / wrinkled seed / wrinkled seed /

yellow cotyledons green cotyledons yellow cotyledons green cotyledons
Ratio 9 3 3 1
▲ Table 16.3 Expected ratio of offspring from a dihybrid cross
plants grown from
homozygous homozygous
round, yellow wrinkled, green
peas peas
all round,
yellow peas
(selfed)
round round wrinkled wrinkled

yellow green yellow green
peas peas peas peas
in the ratio of
9 : 3 : 3 : 1
▲ Figure 16.17 A dihybrid cross
It was noticed that two new combinations (recombinations), not represented in the
parents, appeared in the progeny: either ‘round’ or ‘wrinkled’ seeds can occur with
either ‘green’ or ‘yellow’ cotyledons.
Thus the two pairs of factors were inherited independently. That means either one of a
pair of contrasting characters could be passed to the next generation. This tells us that
a heterozygous plant must produce four types of gametes in equal numbers. This is
explained in Figure 16.18.
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parental (P)
phenotypes: homozygous
round and yellow
homozygous
wrinkled and green 16
genotypes: RRYY rryy pea plants are diploid so they have two
copies of each allele
(meiosis) (meiosis)
gametes: RY ry gametes produced by meiosis so only

have one copy of each allele

offspring (F1)
genotypes: RrYy F1 progeny are heterozygous for

both genes
phenotypes: heterozygous the alleles for ‘round’ and ‘yellow’ are
round and yellow dominant; the F1 progeny are all
round yellow peas
F1 selfed RrYy RrYy genes are on separate

chromosomes and random
(meiosis) (meiosis) assortment occurs i.e.
R may assort with Y or y
r may assort with Y or y
so four different types of gametes
gametes: RY Ry rY ry RY Ry rY ry (both and ) are formed, in equal
proportions (independent
assortment)
1
1 RY 4 RY
4 1
16 RRYY
round 1
1 Ry yellow
4 Ry
4 1 1
16 RRYy 16 RRYy
round round 1
1 rY yellow yellow
4 rY
4 1 1 1
16RrYY 16 RRyy 16RrYY
round round round 1
1 r
y 4 ry
yellow green yellow
4 1
1 1 1
16RrYy 16 RrYy 16 RrYy 16 RrYy
round round round round
yellow yellow yellow yellow random fertilisation between all four
1 1 1
16 Rryy 16 rrYY 16 Rryy gametes produces 9 : 3 : 3 : 1 ratio of
round wrinkled round offspring given many crosses occur
green yellow green
1 1
16 rrYy 16 rrYy
wrinkled wrinkled
yellow yellow
1
16 rryy
wrinkled
green
offspring (F2)
genotypes: 1 RRYY 1 RRyy 1 rrYY 1 rryy

2 RrYY 2 Rryy 2 rrYy
2 RRYy
4 RrYy
genotypes ratio: 9 : 3 : 3 : 1
phenotypes: round round wrinkled wrinkled

▲ Figure 16.18 Genetic diagram showing the behaviour of alleles in the dihybrid cross
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Questions From the dihybrid cross we can conclude a Law of independent assortment:
16 10 In Figure 16.18,
identify the
During meiosis the separation of one pair of alleles is independent of the
separation of another pair of alleles.
progeny that are
recombinants. The dihybrid test cross
11 When a tall, Look back to page 354 to remind yourself of the issue the monohybrid test cross sorts out.
cut-leaved tomato
Why is a test cross sometimes necessary?
plant and a dwarf,
potato-leaved tomato
16 Inheritance
In the case of dihybrid inheritance, too, while homozygous recessive genotypes such
plant were crossed
all their progeny as wrinkled green peas (rryy) can be recognised in the phenotype, homozygous round
were tall and yellow peas (RRYY) and heterozygous round yellow peas (RrYy) look exactly the
cut-leaved. These same (Figure 16.17). They can only be distinguished by the progeny they produce, as
were subsequently illustrated in a dihybrid test cross (Figure 16.19).
crossed and the Unlike the monohybrid test cross where the outcome is a ratio of 1 : 1, in the dihybrid
progeny of this test cross the outcome is a ratio of 1 : 1 : 1 : 1.
second generation
were in the ratio: parental (P) plants grown
• tall and from
phenotypes: homozygous heterozygous
cut-leaved 9 wrinkled peas with round peas with
• tall and green cotyledons yellow cotyledons
potato-leaved 3 genotypes: rryy RrYy
• dwarf and (meiosis) (meiosis)

cut-leaved 3
gametes:
• dwarf and ry ry ry ry RY Ry rY ry
potato-leaved 1
Draw a fully
es
annotated genetic
et
1
m
diagram to show 4 RY
ga
y
lr
al
1
genotypes of the 4 RrYy
parents and progeny. round 4
1
Ry
ga
yellow
m
12 In a breed of cocker
et
1
Rryy
es
4
spaniel black coat round 1
4 rY
(B allele) is dominant green
1
to red coat (b allele) rrYy
4
wrinkled 1
and solid pattern 4 ry
yellow
(S allele) is dominant 1
rryy
to spotted pattern 4
wrinkled
(s allele). green
a What are offspring
the possible
genotypes of a genotypes: RrYy Rryy rrYy rryy
spaniel with a genotypes ratio: 1 : 1 : 1 : 1

solid-patterned
black coat? phenotypes: round round wrinkled wrinkled
b How could you
find out the phenotypes ratio: 25% : 25% : 25% : 25%
genotype of this
▲ Figure 16.19 Genetic diagram showing the behaviour of alleles in the
animal? dihybrid test cross
Gene interaction (epistasis)

A dihybrid cross makes the assumption that the alleles inherited from the two genes
act independently of each other. In reality, it is not as simple as that. Gene interactions
occur, resulting in offspring ratios that are different from the expected 9 : 3 : 3 : 1 ratio.
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Gene interaction is the interplay between the alleles of genes at different loci, which has
an impact on the phenotype of one character. When one gene masks or alters the effect
of another gene this is referred to as epistasis. 16
With two genes, there are four alleles and so 16 pairs, which in an ideal Mendelian
cross should result in a 9 : 3 : 3 : 1 ratio. If a different ratio is observed, you can assume
epistasis is occurring. There are many types of interactions between genes.
When recessive alleles at one locus mask the expression of both
(dominant and recessive) alleles at another locus, this is called
Dihybrid
recessive epistasis. Recessive epistasis yields a typical 9 : 3 : 4 ratio

cross
BbEe BbEe in the F2 cross. (You are not required to know the expected ratios for
different types of epistasis.)
F2
BE
BE
BBEE An example of recessive epistasis is found for grain colour in maize,

or coat colour of Labrador retriever dogs.
Be
Be
BBEe BBEe
Two genes are involved in coat colour determination in Labrador
bE
bE
BbEE BBee BbEE retrievers. Genes BB and Bb result in a black coat, gene bb produces
be
a golden coat. The chocolate coat colour of Labrador retrievers is a

be
BbEe BbEe BbEe BbEe result of homozygosity for a gene that is epistatic to the gene for coat
colour. The epistatic gene has two alleles, the dominant allele (E)
Bbee bbEE Bbee
enables the coat colour allele to be expressed. If the recessive allele
bbEe bbEe (e) is homozygous, coat colour is not expressed on the body but the
nose is black if allele B is present or brown if allele b is homozygous.
bbee Pigment production (B) and subsequent incorporation (E) into the
hair shaft are controlled by two separate genes. For the body coat to
9 black 3 brown 4 golden have a colour expressed, a dominant allele of the epistatic gene, E,
must be present. For the coat to be black, the dominant coat colour
(9 B_E_) : (3 bbE_) : (3 B_ee; 1 bbee) allele B must also be present (Figure 16.20).
▲ Figure 16.20 Dominant epistasis is the effect of a dominant allele of one gene
masking the action of either allele of the other gene. The ratio is
12 : 3 : 1 instead of 9 : 3 : 3 : 1. An example of dominant epistasis is
found for fruit colour in summer squash. There are three types of
fruit colour found in this squash: white, yellow and green. White
Parents White fruit Yellow fruit colour is controlled by the dominant gene W and yellow colour by
WWgg × wwGG
the dominant gene G. White is dominant over both yellow and green.
The green fruits are produced when the genotype is wwgg. A cross
F1 WwGg White fruit between plants having white and yellow fruits produces F1 with white
fruits. A cross of F1 plants produces plants with white, yellow and
green coloured fruits in F2 in a 12 : 3 : 1 ratio (Figure 16.21). This is
G
because W is dominant to w and epistatic to alleles G and g. Hence

W
F2
G
WWGG it will mask the expression of G/g alleles. Thus, in F2, plants with
g
[W]
W
WWGG and WWgg genotypes will produce white fruits; plants with
g
WWGg WWGg
wwGG and wwGg will produce yellow fruits and those with wwgg
G
[W] [W]
w
WwGG WWgg WwGG genotype will produce green fruits. So the normal dihybrid ratio
9 : 3 : 3 : 1 is modified to a 12 : 3 : 1 ratio in the F2 generation.
g
[W] [W] [W]

w
WwGg WwGg WwGg WwGg

[W] [W] [W] [W] Introducing Drosophila
Wwgg wwGG Wwgg
[W] [Y] [W]
The fruit fly (Drosophila) commonly occurs around rotting vegetable
wwGg wwGg material. The most common form is often called the ‘wild type’, to
[Y] [Y] differentiate it from the various naturally occurring mutant forms.
wwgg
[G]
Drosophila has become a useful experimental animal in the study of
genetics because:
[W] = white fruit, [Y] = yellow fruit, [G] = green fruit
» Drosophila has four pairs of chromosomes (Figure 16.22, overleaf)
▲ Figure 16.21 Fruit colour in summer squash » from mating to emergence of adult flies (generation time) only
is an example of dominant epistasis takes about 14 weeks
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» one female produces hundreds of offspring
» fruit flies are relatively easily handled, cultured on sterilised artificial medium in
16 wild type Drosophila glass bottles and they can be temporarily anaesthetised for setting up cultures and
antennae abdomen
sorting progeny.
head thorax wings
ebony body vestigial wing white eye chromosomes of male

mutant mutant mutant and female
3 3
4
16 Inheritance
2 2
X Y
X
compound three pairs A dihybrid cross can be shown in Drosophila, for example by crossing normal flies (wild
eye of legs type) with flies homozygous for vestigial wings and ebony body (Figure 16.23). These
▲ Figure 16.22 Wild type
characteristics are controlled by genes that are not on the sex chromosomes. The genes
Drosophila and some concerned in this Drosophila cross are on different autosomal chromosomes.
common mutants
P Drosophila with Drosophila with
normal wings and normal body vestigial wings and ebony body
(wild type) (mutant form)
all normal wings

F1 normal body
F2 (sibling crosses)
normal wings normal wings vestigial wings vestigial wings

normal body ebony body normal body ebony body
in the ratio of
9 : 3 : 3 : 1
▲ Figure 16.23 A dihybrid cross in Drosophila
Questions
13 Define what is meant by the term mutant organism (or cell).
14 a Construct a genetic diagram for the dihybrid cross shown in Figure 16.23, using
the layout given in Figure 16.18.
b Determine the genotypes of the offspring of the F2 generation.
c Identify which of these are recombinants.
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EXTENSION
Drosophila and the dihybrid cross Drosophila melanogaster (the fruit fly) was first selected
16
by an American geneticist called Thomas Morgan in
Mendel had died in 1884 – in relative obscurity, at least 1908 as an experimental organism for the investigation
as far as the scientific community was concerned. Few of genetics in an animal. Morgan was awarded a Nobel
seemed to know of his scientific work and those who Prize in 1933 because by his experiments he had:
were aware did not appear to understand his results.
» shown that Mendel’s ‘factors’ are linear sequences
But his papers were rediscovered in 1900, as a result of
of genes on chromosomes (what is now called the
careful literature searches by people keen to advance

chromosome theory of inheritance)
our understanding of inheritance. Mendel’s results
» discovered sex chromosomes and sex linkage
came to be confirmed and then extended by many
» demonstrated crossing over and the exchange
others, using a range of species.
of alleles between chromosomes resulting from
chiasmata formed during meiosis.
Probability and chance in genetic crosses

We can see that there is an expected ratio of offspring of 9 : 3 : 3 : 1 when the dihybrid
cross is carried out. Actually, the offspring produced in many dihybrid cross experiment
do not exactly agree with the expected ratio. This is illustrated by the results of an
experiment with mutant forms of Drosophila in Table 16.4.
Phenotypes in F2 generation normal wings, normal wings, vestigial wings, vestigial wings, Total numbers
Predicted ratio 9 3 3 1
Expected numbers of offspring 313 104 104 35 556
Actual numbers of offspring 315 108 101 32 556
▲ Table 16.4 Observed
and expected numbers Clearly, these results are fairly close to the ratio of 9 : 3 : 3 : 1, but they are not exactly in
of offspring from a the predicted ratio, precisely. What, if anything, went ‘wrong’?
dihybrid cross
Well, we can expect this ratio among the progeny only if three conditions are met:
» fertilisation is entirely random
» there are equal opportunities for survival among the offspring
» very large numbers of offspring are produced.
In this experiment with Drosophila, the exact ratio may not have been obtained because,
for example:
» more male flies of one type may have succeed in fertilising females than of the other type
» more females of one type may have died before reaching egg-laying condition than
of the other type
» fewer eggs of one type may have completed their development than of the other types.
Similarly, in breeding experiments with plants such as the pea plant, exact ratios may
not be obtained because of parasite damage or by the action of browsing predators
on the anthers or ovaries in some flowers or because some pollen types fail to be
transported by pollinating insects as successfully as others, perhaps.
The chi-squared test

Experimental geneticists are often in the situation of asking ‘Do the observed values
differ significantly from the expected outcome?’ – for example, for the sort of reasons
discussed above.
This question is resolved by a simple statistical test, known as the chi-squared ( x2) test.
This is used to estimate the probability that any difference between the observed results
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and the expected results is due to chance. If it is not due to chance, then there may be
an entirely different explanation and the phenomenon would need further investigation.
16 The chi-squared statistic is calculated using this formula:
(O 2 E)2 where: O 5 observed result
x2 5 
E
E 5 expected result
( means ‘the sum of’)
The chi-squared test applied

16 Inheritance
We can test whether the observed values obtained from the dihybrid cross between wild
type (normal) Drosophila flies and flies homozygous for vestigial wings and ebony body
(Table 16.5) differ significantly from the expected outcome.
First we calculate x2 (in this example, x2 is 0.47).
Predicted Observed Expected (O 2 E)2

Category ratio number, O number, E O2E (O 2 E)2 E
Normal wings, normal body 9 315 312.75 2.25 5.0625 0.016
Normal wings, ebony body 3 108 104.25 3.75 14.0625 0.135
Vestigial wings, normal body 3 101 104.25 23.25 10.5625 0.101
Vestigial wings, ebony body 1 32 34.75 22.75 7.5625 0.218
Total 556 556 0.470 (x2)
▲ Table 16.5 x2 calculation
We now consult a table of the distribution of x2 to find the probability of obtaining a

deviation by chance alone as large as (or larger than) the one we have.
Question
The table takes account of the number of independent comparisons involved in our test.
15 In the dihybrid Here there were four categories and therefore there were three comparisons made – we
test cross between call this ‘three degrees of freedom (d.f.)’.
homozygous
dwarf pea plants
Degrees of Probability greater than:
with terminal
freedom 0.99 0.95 0.90 0.10 0.05 0.01 0.001
flowers (ttaa) and
heterozygous tall d.f. 5 1 0.0001 0.0039 0.0158 2.706 3.841 6.635 10.83
pea plants with axial d.f. 5 2 0.0201 0.103 0.211 4.605 5.991 9.210 13.82
flowers (TtAa), the
d.f. 5 3 0.115 0.352 0.584 6.251 7.815 11.345 16.27
progeny were:
» tall with axial ▲ Table 16.6 Table of x2 distribution
flowers: 55
» tall with terminal The probability given by the table suggests that the differences between the results we
flowers: 51 expected and the outcome we observed is due to chance.
» dwarf with axial » If the value of x2 is bigger than the critical value highlighted (a probability of
flowers: 49 0.05) then we can be at least 95 per cent confident that the difference between the
» dwarf with observed and expected results is significant.
terminal » If the value of x2 is smaller than the critical value highlighted (a probability of 0.05)
flowers: 53
then we can be confident that the differences between the observed and expected
Use the x2 test to results are due to chance.
determine whether
or not the difference In biological experiments we take a probability of 0.05 or larger to indicate that the
between these differences between observed (O) and expected (E) results are not significant. We can
observed results and say they are due to chance.
the expected results In this example, the value (0.47) lies between a probability of 0.95 and 0.90. This means
is significant. that a deviation of this size can be expected 90–95 per cent of the times the experiment
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is carried out. There is clearly no significant deviation between the observed (O) and the
expected (E) results.
The chi-squared test is similarly applicable to the results of test crosses and monohybrid 16
crosses. However, in any chi-squared test that does not confirm that the results conform
to the anticipated result (i.e. if it gives us a value for x2 that is bigger than the critical
value meaning that the probability of getting that result is smaller than 0.05), then we
must reconsider our explanation of what is occurring. In this outcome, the statistical
test gives no clue as to the actual position or behaviour of the alleles concerned. Further
genetic investigations are required.

EXTENSION
How environment may affect the phenotype
If plants of a tall variety of pea are deprived of nutrients (nitrates and phosphates, for example) in the growing
phase of development, full size may not be reached. A ‘tall’ plant may appear dwarf. The same occurs in humans
who have been seriously and continuously underfed and malnourished as growing children.
Many characteristics of organisms are affected by both the environment and their genotype. In fact the phenotype
is the product of genotype and influences of the environment.
A striking example of this occurs in the honey bee (Apis mellifera). In a colony of honey bees there are three
phenotypes (workers, drones and queen – Figure 16.24), but only two genotypes. The drones are the
community’s males and they develop from unfertilised eggs (their genotype is haploid). The queen and the workers
develop from fertilised eggs and have identical genotypes. The queen, who is a much larger organism, differs from
her workers only by the diet she is fed in the larval stage (an environmental factor). Her protein-rich food is not
given to the larvae that will be workers. This makes a significant difference in their phenotypes.
Queen Worker Drone
the queen lays about 1500 eggs

per day, each in a wax cell
prepared for her by the workers
most eggs are fertilised occasionally eggs that are
unfertilised are laid by the queen.
a very few larvae are fed on ‘royal These still develop into larvae
jelly’ (protein-rich food prepared (with a single set of chromosomes, i.e. haploid).
by the nurse workers) and These larvae are fed on ‘royal jelly’ (briefly),
develop into new queens followed by pollen and nectar; they
larvae fed on pollen and nectar
develop into drones
develop into workers (females
a queen normally survives for with non-functioning drones are fertile males that
2–5 years but mates only once, reproductive organs) survive for about 5 weeks
storing sperms sufficient for her
lifetime in her abdomen workers survive for about drones do no work in the hive
6 weeks in the summer period
their sole role is to compete to
workers undertake a sequence of fertilise a new queen on her
duties, typically: nuptial flight, after which they are
A honey bee community typically consists
of 20 000–80 000 individuals, of which 1. as ‘nurse’ workers: killed or die
the vast majority are workers. tending growing larvae
2. as ‘outside’ workers:
surveying for feeding sites
guard duty at hive entrance
foraging for food and water
communicating about new
food sites to fellow workers
▲ Figure 16.24 Honey bees – two genotypes but three phenotypes
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16.2 continued…The relationship between genes,
16 proteins and phenotype
Learning outcomes
16.2.6 explain the relationship between genes, proteins and phenotype with
respect to the: TYR gene, tyrosinase and albinism; HBB gene, haemoglobin
and sickle cell anaemia; F8 gene, factor VIII and haemophilia; HTT gene,
16 Inheritance
huntingtin and Huntington’s disease

16.2.7 explain the role of gibberellin in stem elongation including the role of the
dominant allele, Le, that codes for a functional enzyme in the gibberellin
synthesis pathway, and the recessive allele, le, that codes for a
non-functional enzyme
Starting point
★ Studies of human genetic conditions have revealed the links between genes,
enzymes and the phenotype.
Investigating human genetics

Studying human inheritance by experimental crosses (by selecting parents, sibling
crosses, and the production of large numbers of progeny) is out of the question.
Instead we may investigate the pattern of inheritance of a particular characteristic
by researching a family pedigree, where appropriate records of the ancestors exist. A
human pedigree chart uses a set of rules. These are identified in Figure 16.25.
Key
male
Generation parents unaffected
female
I male
affected
Richard Judith female
birth sequence of offspring of parental marriage/mating
offspring (siblings)
individuals on the same line
are of the same generation
II
David Anne Louise Charles Alice Henry Sophie
III
Chris Liz James Sarah William Arthur Diana Frederick Gail
IV union of related individuals

(cousins) = consanguinity
Alan Patricia Jessica Timothy Jonathan Mary
▲ Figure 16.25 An example of a human pedigree chart
We can use a pedigree chart to detect conditions likely to be due to dominant

and recessive alleles. In the case of a characteristic due to a dominant allele, the
characteristic tends to occur in one or more members of the family in every generation.
On the other hand, a recessive characteristic is seen infrequently, often skipping many
generations.
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Questions 16 In the human pedigree chart in Figure 16.25:
a who are the female grandchildren of Richard and Judith
b who are Alan’s
16
i grandparents
ii uncles
c how many people in the chart have parents unknown to us
d what are the names of two offspring who are cousins?
17 Explain why conditions controlled by a mutant, dominant allele are likely to appear
16.2 continued…The relationship between genes, proteins and phenotype

in every subsequent generation, but characteristics due to a single recessive allele are
likely to appear infrequently in the family pedigree chart.
TYR gene, tyrosinase and albinism

Albinism is a rare inherited condition of humans (and other mammals) in which the
individual has a block in the biochemical pathway by which the pigment melanin is
formed. Albinos have white hair, very light coloured skin and pink eyes. Albinism shows
a pattern of recessive monohybrid inheritance in humans (Figure 16.26). In the chart
shown of a family with albino members, albinism occurs infrequently, skipping two
generations altogether.
Key
normal albinos
skin colour
Albino people must be Generation

homozygous for the
recessive allele (pp).
People with normal skin 1 2
pigmentation may be
homozygous normal
(PP) or carriers (Pp).
I
carrier carrier carrier
X
II
1 2 3 4 5 6 7 8
III
This is a typical family tree for inheritance of a characteristic controlled by a recessive

allele. In generation I, individual 2 must be pp (albino). In generation II, all offspring
must be carriers (Pp) because they have received a recessive allele (p) from their mother.
IV In generation III, individual 8 must be a carrier and her partner X must also be a carrier,
since their offspring include a son who is albino.
▲ Figure 16.26 Pedigree chart of a family with albino members
A mutation in the TYR gene for the enzyme tyrosinase, in which glutamine is
substituted for arginine at a particular locus, results in a defective gene that fails to code
for the tyrosinase protein. As a consequence, active tyosinase and the pigment melanin
are absent from pigment-forming cells in the body. This has evident impacts on the
phenotype. The mutated allele is recessive, so the albino people are homozygous for the
mutant allele.
HBB gene, haemoglobin and sickle cell anaemia

The smallest form of gene mutation occurs when one base is replaced by another – a
base substitution. An example of this type of gene mutation is the cause of the human
condition known as sickle cell anaemia. It is illustrated in Figure 16.27, overleaf. The
HBB gene that codes for the amino acid sequence of the beta chain of haemoglobin
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The mutation that produces sickle cell haemoglobin (HbS) is
in the gene for β-haemoglobin. It results from the substitution
16 of a single base in the sequence of bases that make up all the

codons for β-haemoglobin.
part of normal gene part of mutated gene

DNA
antisense (coding) strand
(template for transcription C T C C A C substituted
of mRNA) base
sense strand G A G G T G
16 Inheritance
transcription
mRNA, formed by
complementary
base pairing G A G G U G
C U C C A C
tRNA–amino acid complex
showing complementary
anticodons
glutamic valine
acid
part of the resulting protein sequence, translation
showing the amino acid residues
assembled:
Val–His–Leu–Thr–Pro–Glu– Val–His–Leu–Thr–Pro–Val–
(abbreviations for amino acids
shown in Figure 6.11, page 131)
Hb Hbs
drawing based on a photomicrograph of a blood smear,

showing blood of a patient with sickle cells present among
healthy red blood cells
phenotypic appearance
of HbHb red blood cells and
sickle cells (HbsHb)
10 µm
▲ Figure 16.27 Sickle cell anaemia – an example of a gene mutation
occurs on chromosome 11 and is prone to a substitution of the base adenine (A) by

thymine (T) in a codon for the amino acid glutamic acid. As a consequence, the amino
acid valine appears at that point, instead.
The effects on the properties of the haemoglobin molecule of this simple change of one
amino acid residue for another within the whole haemoglobin molecule are dramatic.
The molecules with this unusual haemoglobin (known as haemoglobin Hbs) tend to
clump together and form long fibres that distort the red blood cells into sickle shapes.
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Question In this condition they transport little oxygen and the sickle cells may even block smaller
vessels. People who are heterozygous for the mutated allele (Hb Hbs) have less than 50
18 Explain how the
cause of sickle cell
per cent of the sickle-shaped red blood cells. The person is said to have sickle cell trait
and they are only mildly anaemic. However, people who are homozygous for sickle cell
16
trait and sickle cell haemoglobin (Hbs Hbs) have a serious problem and are described as having sickle cell
anaemia supports the anaemia. Problems with the heart and kidneys are common in people affected with
concept of a gene as sickle cell anaemia.
a linear sequence of
bases. We have already noted the potential advantage in having the sickle cell trait. Malaria is
the most important of all insect-borne diseases (see Figure 10.7, page 205). The malarial
16.2 continued…The relationship between genes, proteins and phenotype

pathogen Plasmodium completes its lifecycle in red blood cells, but it cannot do so in
red blood cells containing the abnormal form of haemoglobin (Hbs). People with sickle
cell trait are protected to a significant extent. Where malaria is endemic in Africa,
possession of one mutant allele (i.e. having sickle cell trait but not sickle cell anaemia) is
advantageous.
Turn back to Figure 10.9 ( page 207) now and note the correlations between the distributions of
the sickle cell allele and of the distribution of malaria in Africa.
So, a person with sickle cell trait has a different phenotype from that of a person with
normal haemoglobin. For example, the former has an improved chance of surviving
malaria in regions where this disease is endemic.
We have just seen that sickle cell anaemia is due to the substitution of a single
nucleotide in one codon of the gene for the protein in the beta chain of haemoglobin.
So sickle cell anaemia is a case of a chance change in the nucleotide sequence in DNA
affecting the amino acid sequence in a protein and the phenotype of the organism.
F8 gene, factor VIII and haemophilia

In the circulatory system of a mammal, if an injury occurs there is a risk of uncontrolled
bleeding. This is normally overcome by the blood clotting mechanism that causes any gap
in a blood vessel to be plugged. Haemophilia is a rare genetically-determined condition in
which the blood does not clot normally. The result is frequent, excessive bleeding.
There are two forms of haemophilia, known as haemophilia A and haemophilia B.
Defects in the F8 gene, which codes factor VIII – an essential blood-clotting protein –
result in haemophilia A.. Today, haemophilia is effectively treated by the administration
of the clotting factor the patient lacks.
Haemophilia is a sex-linked condition because the genes controlling the production of
Question
the blood proteins concerned are located on the X chromosome. Haemophilia is caused
19 Haemophilia is by a recessive allele. As a result, haemophilia is largely a condition of the male, since in
sex-linked condition him a single X chromosome carrying the defective allele (Xh Y) will result in disease. For
that results from the a female to have haemophilia, she must be homozygous for the recessive gene (Xh Xh),
inheritance of an but this condition is usually fatal in utero. It may result in a natural abortion.
allele carried on the
X chromosome. A female with one X chromosome with the recessive allele and one with the dominant
Explain why allele (XH Xh) is a carrier. She has normal blood clotting but for any daughters she has
haemophilia is more with a normal male, there is a 50 per cent chance of them being carriers; for any sons
common in males. there is a 50 per cent chance of them being haemophiliac (Figure 16.28, overleaf).
HTT gene, huntingtin and Huntington’s disease

Huntington’s disease (HD) is due to an autosomal dominant allele on chromosome 4.
The mutation takes the form of repeats of three nucleotides (CAG) between 36 and 120
times at a particular locus in the gene. The function of the HTT gene, or rather of the
protein it codes for – huntingtin – is unclear, but it appears to be active in the brain.
The disease is extremely rare (1 case per 20 000 live births). Affected individuals
are almost certainly heterozygous for the mutant (defective) gene. Appearance of the
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parental (P)
16 phenotypes: carrier female ( ) × normal male ( )
genotypes: XH Xh XH Y
(meiosis) (meiosis)
gametes: 1 XH 1 Xh 1 XH 1 Y
2 2 2 2
)
16 Inheritance
m
(
al
1
es
h
e
et
X 2
ga
1 XH
m
ga
2
et
es
e
1
al
(
XH Xh
m
H 1
)
fe
4
1 X 2 Y
2
1 H H 1
4
X X Xh Y
4
1
XH Y
4
offspring (F1)
genotypes: XH XH XH Xh XH Y Xh Y
phenotypes: normal carrier normal haemophiliac
females males
( ) ( )
▲ Figure 16.28 Genetic diagram showing the inheritance of haemophilia
symptoms is usually delayed until the age of 40–50 years, by which time the affected
person – unaware of the presence of the disease – may have passed a copy of the
dominant allele to one or more of his or her children. Any child of an affected person
has a 50 per cent chance of inheriting the condition.
The disease takes the form of progressive mental deterioration, which is accompanied by
involuntary muscle movements (twisting, grimacing and staring in ‘fear’). A person with
HD then loses all control of his or her mental and physical abilities, and death occurs
within 10 years. The disease is named after the American doctor who first investigated
the condition. There is no known treatment.
The role of gibberellin in stem elongation

Gregor Mendel (1822–84) conducted experiments into the inheritance of a contrasting
characteristics of the garden pea plant, Pisum sativum. For example, the height of stem
in the garden pea plant, which may be either ‘tall’ (say about 48 cm), or ‘dwarf’ (about
12 cm). Ultimately, it was established that this characteristic is controlled by a single
gene with two alleles.
We now know that this height difference between tall and dwarf pea plants is due to
the ability (or otherwise) to convert a precursor molecule of gibberellin into an active
form in the cells of the pea plant. In fact, tall pea plants carry at least one dominant
allele (Le), which codes for a protein that functions normally in the gibberellin-synthesis
pathway, catalysing the formation of gibberellin. As the allele is dominant it may be
present as a single allele or with two but, in either case, gibberellin will be present and
the plant will be tall.
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Dwarf pea plants carry recessive two alleles (le) that code for a non-functional protein.
This enzyme fails in the gibberellin-synthesis pathway. Plants with two recessive alleles
remain dwarf, lacking the supply of gibberellin that enables extension growth in stem
length to occur (Figure 16.29).
16
tall pea plant dwarf pea plant
16.3 Gene control

alleles present: Le Le or Le le alleles present: le le
effect: gibberellin effect: gibberellin

precursor precursor
molecule molecule
functioning non-functioning
enzyme coded enzyme coded
for by Le allele for by le allele
active gibberellin gibberellin absent

▲ Figure 16.29 The role of specific alleles in the control of height in the garden pea
16.3 Gene control

Learning outcomes
16.3.1 describe the differences between structural genes and regulatory genes
and the differences between repressible enzymes and inducible enzymes
16.3.2 explain genetic control of protein production in a prokaryote using the lac
operon (knowledge of the role of cAMP is not expected)
16.3.3 state that transcription factors are proteins that bind to DNA and are
involved in the control of gene expression in eukaryotes by decreasing or
increasing the rate of transcription
16.3.4 explain how gibberellin activates genes by causing the breakdown of
DELLA protein repressors, which normally inhibit factors that promote
transcription
Starting point
★ Some genes are transcribed all the time to produce constitutive proteins;
others are only ‘switched on’ when their protein products are required.
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Regulation of gene expression
16 We have seen that chromosomes are effectively a linear series of genes. We define a gene
as a specific region of a chromosome that is capable of determining or influencing the
development of a specific characteristic of an organism. It is a specific length of the DNA
double helix, hundreds or (more typically) thousands of base pairs long. Remember,
every living cell carries a full complement of genes; this genetic complement constitutes
the genome of the cell or organism.
Consequently, cells and organisms must regulate the particular genes that they express
16 Inheritance
at any given time or stage of development. Unicellular organisms and multicellular

organisms may continually switch on and switch off genes in response to signals from
their external and internal environments. While some genes are actively transcribed
throughout the life of the cell, others are activated (we say they are expressed) only at a
particular stage in the life of the cell, or when the substance they act on (their substrate
molecule) is present, for example. Very many of our genes have to be deliberately
activated, as required. In a multicellular organism, every nucleus contains the coded
information relating to the development and maintenance of all mature tissues and
organs. For example, the genes concerned with development of the organism from the
zygote are some of the first to be expressed, but most probably for a limited period
only. So, both during development and later in the life of the organism, this genetic
information is used selectively. Typically, less than 25 per cent of the protein-coding
genes in human cells are expressed at any time. The expression of genes is related to
when and where the proteins they code for are needed (Table 16.7).
When and why genes are expressed

Expressed all the time genes responsible for routine, continuous metabolic
functions (for example, respiration), common to all
cells, continuous throughout life
Expressed at a selected stage in as cells derived from stem cells are developing into
cell or tissue development muscle fibres or neurones, for example
Expressed only in the mature cell genes responsible for antibody production in a
mature plasma cell, after these have been cloned
Expressed on receipt of an when a particular hormone signal, metabolic signal,
internal or external signal or nerve impulse is received by the cell, such as the
gene for insulin production in β cells in the islets of
Langerhans
▲ Table 16.7 Gene regulation – some examples
How is this regulation brought about?

Regulation of gene action is partly regulated by the genes themselves. While the role
of many genes is to code for specific enzymes or proteins required by working cells at
some stage, others are different – their role is to regulate other genes. Consequently, we
can recognise two categories of gene:
» Structural genes code for a structural protein, or an enzyme, or an RNA molecule
not involved in regulation. They are required by cells to create or maintain the
structure, or enable the functioning, of the cell or organism. They are transcribed
into proteins.
» Regulatory genes are involved in controlling the expression of one or more genes.
They may code for a protein or for an RNA molecule.
Genes are also regulated by ‘signals’ from the environment – typically from within the
cell. These act on the enzymes or on the genes that code for them. Consequently, we can
recognise two categories of enzymes:
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» Inducible enzymes are produced under specific conditions, such as the presence of
a particular substrate. This substance controls the expression of one or more genes,
structural genes, involved in the metabolism of that substance. In the absence of the 16
substrate, gene action is switched off.
» Repressible enzymes are generally produced continuously, but their production can
be halted. They are formed unless a signal, such as an excess of product, turns their
production off.
Case studies in gene regulation
16.3 Gene control

1 Genetic control of protein production in a prokaryote,
using the lac operon
The lac operon (lactose operon) is a mechanism that ensures that the enzymes required
for the metabolism of lactose are produced only in the presence of lactose. It has been
observed in bacteria, such as E. coli.
This mechanism involves a repressor molecule (coded for by a regulator gene), an
operator gene situated close to the gene that is being regulated (a structural gene, in
this case coding for the lactose metabolising enzyme), and a promoter gene. In the
absence of lactose, the repressor binds to the operator and prevents transcription of the
structural gene. However, if lactose is present, for example, when it becomes available
in the medium in which the bacteria is growing, then the lactose molecule reacts with
the regulator protein, preventing its binding with the operator gene. As a result, the
lactose-metabolising gene is transcribed, and lactose is metabolised. Once all the lactose
has been used up, the repressor molecule blocks transcription again. The mechanism is
illustrated in Figure 16.30.
This type of mechanism occurs in prokaryotes (bacteria and cyanobacteria) only.
In eukaryotes the regulator-gene mechanisms are more complicated.
In the presence of the substrate lactose:
1 Lactose has combined with the repressor
lactose and inhibited its action.
2 RNA polymerase has bound to the

promoter and is about to express the
repressor structural gene for lactase. mRNA for
lactase synthesis will be transcribed,
and pass straight to ribosomes in the
surrounding cytoplasm, where lactase
RNA polymerase is synthesised.
operator gene for lactase
promoter 3 Eventually, all the lactose will have
been metabolised, and the repressor
The gene is turned on. will be free to bind to the operator again.
In the absence of the substrate lactose: 1 There is no lactose to combine with

the repressor.
2 The repressor binds with the operator.
3 The RNA polymerase is obstructed

from binding to the promoter.
The gene is turned off.

▲ Figure 16.30 The lac operon and gene regulation
2 Regulation in eukaryotes by enhancers and transcription factors

In eukaryotes, before mRNA can be transcribed by the enzyme RNA polymerase it first
binds together with a small group of proteins called general transcription factors at a
sequence of bases known as the promoter. Promoter regions occur on DNA strands just
before the start of a gene’s sequence of bases. (The promoter is an example of a length
of non-coding DNA with a special function.) Only when this transcription complex of
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proteins (enzyme + factors) has been assembled can transcription of the template strand
of the gene begin. Once transcription has been initiated, the RNA polymerase moves
16 along the DNA, untwisting the helix as it goes, and exposing the DNA nucleotides so
that RNA nucleotides can pair, and the messenger RNA strand be formed and peel way.
The rate of transcription may be increased (or decreased) by the binding of specific
transition factors on the enhancer site for the gene. The position of an enhancer site of
a gene is shown in Figure 16.31. This is at some distance ‘upstream’ of the promoter
and gene sequence. However, when activator proteins bind to this enhancer site a
new complex is formed and makes contact with the polymerase–transcription factor
16 Inheritance
complex. Then the rate of gene expression is increased.

Regulator transcription factors, activators and RNA polymerase are all proteins, and are
coded for by other genes. It is clear that protein–protein interactions play a key part in
the initiation of transcription in eukaryotes.
general
transcription RNA
factors polymerase
activators
coding segment
attach here attach here
(of exons and introns)
enhancer promoter transcription

transcription
termination
start site
region
activators
RNA transcription
active transcription initiation
complex (factors + enzyme)
on the promoter
The lower part of the figure shows a portion of the upper DNA molecule with the activator (orange) region, promotor
(green) region and coding (blue) region. The DNA is looped so that it comes into contact with different parts of the
transcription initiation complex. The complex consists of several proteins and other factors hence the multiple
overlapping spheres (blue). The activator (pink) is also part of the complex. These spheres have been drawn transparent
so that contact with the DNA molecule can be shown.
▲ Figure 16.31 Control sites and the initiation of transcription

07_10 Biology for the IB Diploma Second edition
How gibberellin activates genes
Barking Dog Art
Gibberellin (GA) regulates and promotes many aspects of plant growth and development
(page 337). Remind yourself of some of the roles of GA now.
It is now known that a significant cause of restraint on many aspects of plant growth and
development is the presence of a group of nucleus-based proteins called DELLA proteins.
These proteins are coded for by specific regulatory genes, and they function in the
nucleus itself as powerful transcription factors. How these proteins regulate transcription
is poorly understood, but it has been shown that, when GA levels rise in a plant, DELLA
proteins are deactivated and the plant grows. For example, GA has this effect as it triggers
expression of genes coding for hydrolytic enzymes that convert starch stores to glucose in
germinating seeds such as maize and barley (Figure 15.22, page 340).
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The way that GA controls the levels of growth-repressing DELLA proteins is apparently
by labelling them with a molecule known as ubiquitin. With this marker attached, a
DELLA protein is identified and promptly destroyed by a nucleus-based complex, which
has the role of degrading unneeded or damaged proteins present in the nucleus.
16
SUMMARY
» Genetics is the study of inheritance. Many outcome is a ratio of 1 : 1 and in the dihybrid test
16.3 Gene control

characteristics of organisms are controlled by cross the outcome is a ratio of 1 : 1 : 1 : 1.
the genes which occur as a linear series along » Sex is determined in humans by the sex
chromosomes. Diploid organisms contain chromosomes: XX in the female and XY in the
two copies of each gene in each of their cells. male. The X chromosome is longer than the Y
Alternative forms of a gene are called alleles. and has genes not present on the Y chromosome.
In sexual reproduction, gametes are formed In the male, recessive alleles on the single X
containing one copy of each gene. Offspring chromosome cannot be masked as they often are
formed from the zygote resulting from by dominant alleles in the female. Consequently,
fertilisation receive two copies of each gene (two a number of rare recessive conditions are sex-
alleles), one from each parent. linked and occur more frequently in males. These
» Meiosis is the reductive nuclear division in which, include red–green colour blindness, haemophilia
after cell division, the nucleus present in each and Duchenne muscular dystrophy.
of the four daughter cells formed has half the » Exceptions to the monohybrid ratio arise from
chromosome number of the parent cell, typically alleles which are codominant (rather than there
one of each type. Meiosis is associated with sexual being one dominant and one recessive allele). In
reproduction and the production of gametes. addition, the existence of more than two alleles for
» Alleles may be dominant or recessive or show a gene, known as multiple alleles, complicates
codominance. An organism with two identical inheritance. The human ABO blood group is an
alleles of a gene is homozygous for that gene; example of the latter. It is determined by two of
an organism with different alleles of a gene is three possible alleles which gives four possible
heterozygous. The genetic constitution of an phenotypes, blood groups A, B, AB and O.
organism is its genotype. The resulting appearance » A dihybrid cross concerns the inheritance of
of the organism, its visible and measurable two pairs of contrasting characteristics located
features, is called its phenotype. on different chromosomes. The results confirm
» In a monohybrid cross the inheritance of a that each allele of a gene is equally likely to be
contrasting characteristic controlled by a single inherited with each allele of another gene, a
gene (such as tall and dwarf height in garden pea reflection of the independent assortment of
plants) is investigated. When parents homozygous chromosomes that occurs in meiosis.
for a contrasting characteristic are crossed, the » The environmental conditions experienced by
first generation (F1) will be heterozygous The an organism may also influence the expression
characteristic they show, such as ‘tall’ in the pea, of alleles. A genetically tall organism deprived
will establish that the allele for ‘tall’ is dominant of sufficient nutrients and so develops a
over the allele for ‘dwarf’, which is recessive. phenotype that is short is an obvious example.
When the F1 generation self-fertilise (or sibling Characteristics influenced by the environment
crosses are made in animals), a recessive may show a degree of continuous variation.
characteristic re-emerges in a minority of the » Mutations may also affect the phenotype. When the
offspring, in the ration of 3 : 1 (provided many nucleotide sequence in the DNA of a chromosome
offspring are produced). This shows that only one is changed it may lead to alteration in the amino
allele of a gene is carried in a single gamete. acid sequence of proteins formed in the cell. The
» Since the genotype of an organism showing consequence may be a different phenotype.
dominant characteristics may be homozygous or » Some genes are transcribed all the time, while
heterozygous for the gene concerned, the genotype others are only switched on when their products
of this organism must be determined by a test cross are required. Regulatory genes control the timing
with an organism that is homozygous recessive for of the expression of other genes whose roles are
the characteristic. In the monohybrid test cross the to create and maintain the structure or functions
of the cell or organism.
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16 1 The Labrador retriever is a modern breed of dog that can have yellow, black or
brown fur and pale, black or brown noses. The inheritance of fur and nose colour
is the result of the interaction between genes at two different loci, the B locus and
the E locus.
Figure 1.1 shows a Labrador retriever.

16 Inheritance
▲ Fig. 1.1
Table 1.1 shows how gene interaction results in different phenotypes.
Alleles at B locus Alleles at E locus Phenotype

B_ ee Yellow fur
Black nose
bb ee Yellow fur
Pale nose
B_ E_ Black fur
Black nose
bb E_ Brown fur
Brown nose
Table 1.1
A male Labrador retriever, heterozygous at the B locus and homozygous

recessive at the E locus, was mated with a female Labrador retriever
heterozygous at both loci.
a Explain the terms locus and homozygous. [2]
b Use a genetic diagram to show the possible genotypes and phenotypes of
the offspring from the mating between the two Labrador retrievers. [6]
parental phenotypes
parental genotypes
gametes
offspring genotypes and phenotypes
[Total: 8]
2 In mice, the intensity of pigmentation of the fur is controlled by multiple
alleles of a single gene.
The alleles are listed below in order of dominance, with C as the most dominant.
» C = full colour
» Cch = chinchilla
» Ch = Himalayan
» Cp = platinum
» Ca = albino
a Explain how multiple alleles arise. [2]
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b Eye colour in mice is controlled by two alleles of a single gene, B/b:
» allele B codes for black eyes
» allele b codes for red eyes. 16
A mouse with full colour fur and black eyes was crossed with a mouse with
himalayan fur and black eyes. One of the offspring was albino with red eyes.
Using the symbols above, draw a genetic diagram to show the genotypes and
phenotypes of the offspring of this cross. [6]
[Total: 8]

3 a Explain what is meant by a gene mutation due to base substitution. [4]
b In the inheritance of sickle cell anaemia, the normal allele is represented by
Hb and the sickle cell allele by HbS. Draw and complete a genetic diagram to
explain the genotypes and phenotypes and the proportions of each resulting
from a cross between two individuals of genotype Hb HbS. [8]
c A study of a local population in a central African country found that in a
sample of 12 5000 people:
9449 were homozygous for normal haemoglobin (Hb Hb)
3020 had sickle cell trait (Hb HbS)
31 had sickle cell anaemia (HbS HbS)
Comment on the distribution of the sickle cell allele within this population,
and on any environmental factors that may influence it. [8]
[Total: 20]
4 a List four differences between the processes of mitosis and meiosis,
and state briefly the significance of each. [8]
b Where would you expect
i mitosis and
ii meiosis
to occur in a fully grown flowering plant? [2]
c For a cell with two chromosomes draw diagrams to show:
i metaphase of mitosis
ii metaphase I of meiosis
iii prophase II of meiosis
iv metaphase II of meiosis [4]
d Define the term ‘phenotype’ and explain with reference to an example,
how the environment may affect phenotype. [4]
[Total: 18]
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A LEVEL

In 1858, Charles Darwin Learning outcomes

and Alfred Russel Wallace
proposed a theory of natural
selection to account for the 17.1.1 explain, with examples, that phenotypic variation is due to genetic factors
evolution of species. A year or environmental factors or a combination of genetic and environmental
later, Darwin published factors
On the Origin of Species, 17.1.2 explain what is meant by discontinuous variation and continuous variation
providing evidence for the 17.1.3 explain the genetic basis of discontinuous variation and continuous
way in which aspects of the
variation
environment act as agents
of selection and determine 17.1.4 use the t-test to compare the means of two different samples (the
which phenotypic forms formula for the t-test will be provided, as shown in the Mathematical
survive and which do not. requirements)
The individuals best adapted
to the prevailing conditions
are most likely to succeed in Starting points
the ‘struggle for existence’.
★ The variation that exists within a species is categorised as continuous and
discontinuous.
★ The environment has considerable influence on the expression of features
that show continuous (or quantitative) variation.
17.1 Variation
Introducing variation
Individuals of a species are strikingly similar, which is how we may identify them,
whether humans, buttercups or houseflies, for example. But individuals also show many
differences, although we may have to look carefully in members of species other than
our own. Within families there are remarkable similarities between parents and their
offspring, but no two members of a family are identical, apart from identical twins.
About these differences we can consider:
» genetic factors: some differences may be controlled by genes – such as human blood
groups
» environmental factors: other differences between individuals may be due to the
effect of our environment, such as the fur colour of the Arctic hare or the Siamese cat
» a combination of genetic and environmental factors: other differences between
individuals may be due to both genetics and environment, such as our body height
and weight.
Another important point about variation is that it is of two types (Figure 17.1).
» Discontinuous variation arises when the characteristic concerned is one of two or
more discrete types with no intermediate forms. Examples include the garden pea
plant (tall or dwarf) and human ABO blood grouping (group A, B, AB or O). These
are genetically determined.
» Continuous variation results in a continuous distribution of values. Height in
humans is a good example. Continuous variation may be genetically determined, or
it may be due to environmental and genetic factors working together.
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Dwarf and tall peas
discontinuous variation
The heights of these plants fall into two discrete groups, in both of which there is a
normal distribution of variation, but with no overlap between the groups.
17
20
dwarf tall
16
number of plants
12
17.1 Variation
8
16 24 32 40 48 56
height/cm
(The same number of dwarf and tall plants were measured.)
Human height 50
continuous variation
40
number of people
The results for variation in 30

the height of adult humans
cluster around a mean value
20
and show a normal
distribution. For the purpose
of the graph, the heights are 10
collected into arbitrary groups,
each of a height range of 2 cm.
0
2 4 6 8 0 2 4 6 8 0 2 4 6
0– 2– 4– 6– –7 0– 2– 4– 6– –8 0– 2– 4–
16 16 16 16 168 17 17 17 17 178 18 18 18
height (in 2 cm bands)
▲ Figure 17.1 Discontinuous and continuous variation
Genetic basis of discontinuous variation

We began the story of genetics in Topic 16 with an investigation of the inheritance
of height in the garden pea (page 351), where one gene with two alleles gave tall or
dwarf plants. This clear-cut difference in an inherited characteristic is an example of
discontinuous variation in that there is no intermediate form, and no overlap between
the two phenotypes. There are other examples of discontinuous variation in the
introduction to monohybrid and dihybrid inheritance in that topic.
Genetic basis of continuous variation

In fact, very few characteristics of organisms are controlled by a single gene. Mostly,
characteristics are controlled by a number of genes. Groups of genes that together
determine a characteristic are called polygenes. Polygenic inheritance is the inheritance
of phenotypes that are determined by the collective effect of several genes. The genes
that make up a polygene are often (but not necessarily always) located on different
chromosomes. The effects of any one of these genes make a very small or insignificant
effect on the phenotype, but the combined effect of all the genes of the polygene is to
produce infinite variety among the offspring.
Many features of humans are controlled by polygenes, including body weight and height
(Figure 17.1, above), but also, human skin colour.
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The colour of human skin is due to the amount of the pigment called melanin that is
produced in the skin. Melanin synthesis is genetically controlled. It seems that three,
17 four or more separately inherited genes control melanin production. The outcome is a
continuous distribution of skin colour from very pale (presence of no alleles coding for
melanin production) to very dark brown (all ‘skin colour’ alleles coding for melanin
production). In our illustration of polygenic inheritance of human skin colour, we have
used only two independent genes. This is because dealing with, say, four genes becomes
impossibly unwieldy, on the printed page. Also, the principle can be demonstrated
clearly enough using just two genes (Figure 17.2).
Parents
phenotype: white black
genotype: aabb AABB
F1 generation AaBb
medium
breeding with individual
of same skin colour genotype
F2 generation
ga
es
m
et
et
m
es
ga
AB AB
Ab AABB Ab
aB AABb AABb aB
ab AaBB AAbb AaBB ab
AaBb AaBb AaBb AaBb
Aabb aaBB Aabb
aaBb aaBb
aabb
range of aabb Aabb AAbb AaBB AABB

genotypes: aaBb AaBb AABb
aaBB
range of white light medium dark black

phenotypes:
▲ Figure 17.2 Human skin colour as a characteristic controlled by two independent genes –
an illustration of polygenic inheritance
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How the environment may affect the phenotype
Many characteristics of organisms are affected by both the environment and their
genotype. In fact:
17
phenotype = genotype + influences of the environment
For example, if plants of a tall variety of a pea are deprived of nutrients (nitrates and
phosphates, for example) in the growing phase of development, full size may not be
reached. A ‘tall’ plant may appear dwarf.
When the wind-dispersed seeds of the dandelion plant (Taraxacum officinale) land and
17.1 Variation
germinate in contrasting habitats such as in fully sunlit wasteland, in shaded woodland
soil, or in a crevice on a wall, the forms of the resulting plants when fully grown reflect
the different environmental influences (Figure 17.3).
in soil, in full sunlight in shaded woodland soil in a rocky site
▲ Figure 17.3 Dandelion plant (Taraxacum officinale) plants in contrasting habitats
A further, striking example of the influence of environment on adult form occurs in

the honey bee (Apis mellifera). In a colony of honey bees there are three phenotypes
(workers, drones and queen), but only two genotypes. This was shown in Figure 16.24,
on page 367. The drones are the community’s males and they develop from unfertilised
eggs (their genotype is haploid). The queen and the workers develop from fertilised eggs
and have identical genotypes. The queen, who is a much larger organism, differs from
her workers only by the diet she is fed in the larval stage (an environmental factor).
Her protein-rich food, prepared for her by the nurse worker bees in the colony, is not
available to the larvae that will be workers. This makes a hugely significant difference in
their phenotypes.
Using the t-test to compare the variation of two different

populations
Statistical tests typically compare large, randomly selected representative samples of
normally distributed data. In practice it is often the case that data can only be obtained
from quite small samples.
The t-test may be applied to sample sizes of more than five and less than 30 of normally
distributed data. It provides a way of measuring the overlap between two sets of data – a
large value of ‘t’ indicates little overlap and makes it highly likely there is a significant
difference between the two data sets. An example will illustrate the method. However,
you should note that you are not expected to calculate values of t.
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Applying the t-test
17 An ecologist was investigating woodland microhabitats, contrasting the communities

in a shaded position with those in full sunlight. One of the plants was ivy (Hedra helix),
but relatively few occurred at the locations under investigation. The issue arose: were the
leaves in the shade actually larger than those in the sunlight?
Leaf widths were measured, but because the size of the leaves varied with the position
on the plant, only the fourth leaf from each stem tip was measured. The results from the
plants available are shown in Table 17.1.
Size-class/mm Sun leaves (A) Shade leaves (B)

20–24 24
25–29 26, 26 26
30–34 30, 31, 31, 32, 32, 33 33, 34
35–39 37, 38 35, 35, 36, 36, 36, 37
40–44 43 41, 42
45–49 45
▲ Table 17.1 Sizes of sun and shade leaves of Hedera helix
Steps to the t-test:

1 The null hypothesis assumes the difference under investigation has arisen by
chance; in this example the null hypothesis is:
‘There is no difference in size between sun and shade leaves.’
The role of the statistical test is to determine whether to accept or reject the null
hypothesis. If it is rejected here, we can have confidence that the difference in the
leaf sizes of the two samples is statistically significant.
Next, check that the data are normally distributed. This is done by arranging the data
for sun leaves and shade leaves as in Table 17.1 (and plotting a histogram, if necessary).
2 You are not necessarily expected to calculate values of t. This is a statistic, which, when
required can be found by using a scientific or statistics calculator, or by means of a
spreadsheet incorporating formulae. Actually, a formula for the t-test for unmatched
samples (data sets a versus b) is:
|x – x |
t = a2 b
sa sb2
1
na nb
where:
xa = mean of data set a
xb = mean of data set b
sa2 = standard deviation for data set a, squared
sb2 = standard deviation for data set b, squared
na = number of data in set a
nb = number of data in set b
√ = square root of
3 Once a value of t has been calculated (the value of t here is 2.10) we determine the
degrees of freedom (d.f.) for the two samples, using the formula:
d.f. = (total number of values in both samples) 2 2
= na 1 nb 2 2
In this case, d.f. 5 11 1 11 5 22.
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decreasing value of p
Degrees of
freedom
p values
17
(df) 0.10 0.05 0.01 0.001
1 6.31 12.71 63.66 636.60

2 2.92 4.30 9.92 31.60
3 2.35 3.18 5.84 12.92
4 2.13 2.78 4.60 8.61
5 2.02 2.57 4.03 6.87
17.1 Variation
6 1.94 2.45 3.71 5.96
7 1.89 2.36 3.50 5.41
8 1.86 2.31 3.36 5.04
9 1.83 2.26 3.25 4.78
10 1.81 2.23 3.17 4.59
12 1.78 2.18 3.05 4.32

14 1.76 2.15 2.98 4.14
16 1.75 2.12 2.92 4.02
18 1.73 2.10 2.88 3.92
20 1.72 2.09 2.85 3.85
22 1.72 2.08 2.82 3.79

24 1.71 2.06 2.80 3.74
26 1.71 2.06 2.78 3.71
28 1.70 2.05 2.76 3.67
30 1.70 2.04 2.75 3.65
40 1.68 2.02 2.70 3.55
60 1.67 2.00 2.66 3.46
120 1.66 1.98 2.62 3.37
1.64 1.96 2.58 3.29
p > 0.05 p < 0.05 p < 0.01 p < 0.001
not significant highly very

significant significant highly
(NS) significant
(fairly (very (almost

confident) confident) certain)
▲ Figure 17.4 Critical values for the t-test
4 A table of Critical values for the t-test is given in Figure 17.4. We look down
the column of significance levels (p) at the 0.05 level until you reach the line
corresponding to d.f. = 22. You will see that here, p = 2.08.
5 Since the calculated value of t (2.10) exceeds this critical value (2.08) at the 0.05
level of s ignificance, it indicates that there is a lower than 0.05 probability (5%) that
the difference b etween the two means is solely due to chance. Therefore, we can
reject the null hypothesis, and conclude the difference between the two samples is
significant.
6 For the experimenter, the significance of this statistic is there is a reason for the
difference in the means, which can be further investigated and fresh hypotheses
proposed.
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17.2 Natural and artificial selection
17.2.1 explain that natural selection occurs because populations have the
capacity to produce many offspring that compete for resources; in the
‘struggle for existence’, individuals that are best adapted are most likely
to survive to reproduce and pass on their alleles to the next generation
17.2.2 explain how environmental factors can act as stabilising, disruptive and
directional forces of natural selection

17.2.3 explain how selection, the founder effect and genetic drift, including the
bottleneck effect, may affect allele frequencies in populations
17.2.4 outline how bacteria become resistant to antibiotics as an example of
natural selection
17.2.5 use the Hardy–Weinberg principle to calculate allele and genotype
frequencies in populations and state the conditions when this principle
can be applied (the two equations for the Hardy–Weinberg principle will
be provided, as shown in the Mathematical requirements)
Starting point
★ Populations of organisms have the potential to produce large numbers of
offspring, yet their numbers remain fairly constant year after year.
Competition for resources

Resources of every sort are limited and organisms compete for them. Plants compete for
space, light and mineral nutrients. Animals compete for food, shelter and a mate. To lose
out in the competition for resources means the individual grows and reproduces more
slowly. In extreme cases, they die.
It is also the case that organisms are capable of producing many more offspring than
survive to be mature individuals (Table 17.2). The phrase struggle for existence
neatly sums up the fact that there is an overproduction of offspring in the wild, but
only limited resources to support them.
Organism Number of offspring

Rabbit 8–12
Great tit 10
Cod 2–20 million
Honey bee (queen) 120 000
Poppy 6000
How many of these offspring survive to breed themselves?
▲ Table 17.2 Numbers of offspring produced
Consequently, in a stable population parent generations give rise to a single breeding

pair of offspring, on average. All their other offspring may become casualties of the
‘struggle’. So, populations do not show rapidly increasing numbers in most habitats, or
at least, not for long.
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Classifying ‘competition’ – some terms
Organisms interact with their non-living surroundings and in some situations it may
be these conditions that limit the growth of a population. These are known as the 17
abiotic environment. They include both the chemical and physical components of the
environment – factors such as light, temperature, water and soil. All of these can be
affected by the climate and seasonal changes.
On the other hand, the interactions that occur between organisms are known as biotic
Question
factors. These include competition for space and for resources and may involve predation or
1 Examine the results grazing and parasitism.

of the ecological
study shown in
Figure 17.5, and then Case studies in competition
suggest: 1 Plankton populations fluctuate naturally
a two mineral In practice, populations typically show large fluctuations in their numbers over a period
nutrients in of time. We see a good example of this in the phytoplankton (primary producers) and
the lake water zooplankton (primary consumers) observed in a freshwater lake in a part of the world
that would be with a temperate, seasonal climate. One such community was analysed for a 12-month
taken up by period. Look carefully at the curves on the graph in Figure 17.5.
phytoplankton
and facilitate their nutrients producers nutrients
rapid growth rate (phytoplankton)
in March and
April
increasing quantity
b why the numbers

light
of phytoplankton light
decrease rapidly
by May and temperature
temperature
June, despite
the favourable
conditions of light primary consumers
and temperature (zooplankton)
c the most likely J F M A M J J A S O N D

source of months
the increase ▲ Figure 17.5 Plankton of a freshwater lake, with data on abiotic factors
in nutrients
that begins in We can see there is a significant ‘bloom’ in the phytoplankton population in the third
October. and fourth months of the year and that a corresponding surge in the zooplankton
population occurs shortly afterwards. Note that the abiotic factors of nutrients, light and
temperature were also measured and recorded.
Question 2 The introduction of the rabbit to Australian

2 a How is it that grasslands – an ecological disaster
a non-native A very few wild rabbits were imported from Britain and released in Australia in 1859.
(introduced)
Before that time there were no rabbits in Australia, yet rabbits very rapidly became the
species may
dominant herbivorous mammals of the grasslands of Victoria and New South Wales.
rapidly become
They had reached the Northern Territory of Australia by 1900.
the most common
species in a new Why was this so?
environment?
Apparently the environment in Australia provided the rabbits with all they required.
b What factors At the same time, natural predators and parasites of the rabbit had not arrived in
may later result large numbers and become established. The resulting population explosion caused the
in the non-
destruction of the natural vegetation, the extinction of many plant species and erosion
native species
of top soil. The loss of many native marsupial species followed. Domestic livestock was
decreasing in
threatened, too. This was because ten rabbits or fewer typically consume the equivalent
numbers?
that one adult sheep requires.
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Rabbits are territorial and within their territory, a dominant male mates with most of
the females. The gestation period of a rabbit is 28–30 days. A mature female may have
17 eight or more young per litter and five or six litters are possible in a good season. Juvenile
rabbits will migrate from their parental territory to establish new territories of their own
depending on seasonal conditions and the availability of suitable conditions elsewhere.
In 1950, a biological control agent, the myxomatosis virus, was introduced (Figure 17.6).
Initially it wiped out between 95 and 100 per cent of the rabbits in some areas. However,
rabbit populations eventually recovered as resistance to the myxomatosis virus spread
among the rabbits. Later, the introduction of other specific viral diseases helped control
populations, but again, the rapid appearance of resistance has left rabbits as a formidable
pest in Australia.
a) b)
Question
3 What annotations
could you add to the
graph in Figure 17.7: ▲ Figure 17.6 a) Overpopulation of rabbits in Australia, b) A terminal case of myxomatosis
a to the rising side
3 Prey–predator population oscillation
to a peak of a
predator curve Evidence for naturally occurring changes in the populations of prey and predator came
b to the declining from the record of fur skins (pelts) received by the Hudson Bay Trading Company of
side of a predator Canada from trappers over a 100-year period. The data are for lynx (predator) and
curve snowshoe hare (prey). At that time, hunters of these wild animals survived and made
a living by trading in the skins they had collected from the wild mammals they had
to interpret and
explain the results been able to trap in and around the forests of northern Canada each year. This type of
shown? evidence assumes that the size of the annual catch is directly related to the numbers of
these mammals in the wild population in the years concerned.
Key
160
140
120 snowshoe lynx

hare
numbers / thousands
100
80
60
40
20
0
1845 1855 1865 1875 1885 1895 1905 1915 1925 1935 1945
year
▲ Figure 17.7 Pelts received from trappers at the Hudson Bay Company over a 100-year period
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We can conclude from these three contrasting situations that natural populations have
the potential to increase rapidly in numbers provided they have access to the essential
resources they require. However, the size of a population is eventually limited by
restraints that we can call environmental factors. These factors include space, light and
17
the availability of food. The interactions of predators or parasites with a population may
be equally influential in determining the size of a population. It is this never-ending
competition that results in the majority of organisms failing to survive and reproduce. In
effect, the environment appears to be able to support a certain number of organisms and
the number of individuals in a species remains more or less constant over a period of
time. Competition is a major fact of life for the living world.

Natural selection and speciation
Natural selection operates on individuals, or rather on their phenotypes. Phenotypes
are the product of a particular combination of alleles, interacting with the effects of the
environment of the organism. Consequently, natural selection causes changes to gene
pools. For example, individuals possessing a particular allele or combination of alleles,
may be more likely to survive, breed and pass on their alleles. Individuals that are less
well adapted may not survive or be successful enough to pass on their genes. This process
is referred to as differential mortality. Actually, whether the individual lives or dies is
not important. What is relevant is whether or not their alleles are passed on to the next
generation.
So, natural selection operates to change the composition of gene pools, but the effect of
this varies. We can recognise different types of selection.
Stabilising selection
Stabilising selection occurs when environmental conditions are largely unchanging.
Stabilising selection does not lead to evolution. It is a mechanism which maintains a favourable
characteristic and the alleles responsible for them, and eliminates variants and abnormalities
that are useless or harmful. Probably most populations undergo stabilising selection.
The birth weight of humans is influenced by environmental factors

(e.g. maternal nutrition, smoking habits, etc.) and by inheritance
(about 50%).
When more babies than average die at very low and very high birth weights, This is an example of
this obviously affects the gene pool because it tends to eliminate genes for stabilising selection in
low and high birth weights. that the values (weights)
at the extremes of a
the main graph shows the continuous variation are
birth weights of infants at a selective disadvantage.
born in a London hospital This means that infants of
1935–1946 (histogram) these birth weights are
and the death rate in more likely to die in infancy.
relation to birth weight
20 (broken line) 100
70
50
The data are an example
of continuous variation.
percentage of population
The ‘middleness’ or 15 30
central tendency of this 20
mortality/%
type of data is expressed

in three ways:
10 10
1 mode (modal value) –
the most frequent 7
value in a set of values 5
2 median – the middle
value of a set of values 3
5
where these are
arranged in ascending 2
order
3 mean (average) – the
sum of the individual
values, divided by the 1 2 3 4 5 6 7 8 9 10 11
number of values birth weight/lb
▲ Figure 17.8 Birth weight and infant mortality: a case of stabilising selection
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The example shown in Figure 17.8 comes from birth records of human babies born between
1935 and 1946 in a London hospital. It shows there was an optimum birth weight for babies
17 and those with birth weights heavier or lighter were at a selective disadvantage.
Directional selection
Directional selection may result from changing environmental conditions. In these
situations the majority of an existing form of an organism may no longer be best suited
to the environment. Some other, alternative phenotypes may have a selective advantage.
An example of directional selection is the development of resistance to an antibiotic
by bacteria (Figure 17.9). Certain bacteria cause disease and patients with bacterial
infections are frequently treated with an antibiotic to help them overcome the
infection. Antibiotics are very widely used. However, in a large population of a species
of bacteria, some may carry a gene for resistance to the antibiotic in use. Sometimes
such a gene arises by spontaneous mutation. Sometimes the gene is acquired in a form
of sexual reproduction between bacteria of different populations.
A ‘resistant’ bacterium has no selective advantage in the absence of the antibiotic
and must compete for resources with non-resistant bacteria. But when the antibiotic
is present, most bacteria of the population are killed. Resistant bacteria remain and
create the future population, all of which now carry the gene for resistance to the
antibiotic. The genome has been changed abruptly.
Figure 17.9 Multiple pathogenic bacteria

cell carries gene for resistance
antibiotic resistance in
to an antibiotic (bacterium
bacteria able to inactivate antibiotic) antibiotic-resistant gene acquired
by mutation
pathogen invades and triggers disease

in human (or in a pet or farm animal)
treated with antibiotic, e.g. penicillin

most bacterial cells are killed
but antibiotic-resistant cell survives
gives rise to a new population of

antibiotic-resistant bacteria
(non-resistant competitor
bacteria have been killed,
so there is no competition
for resources)
process is repeated in another %

antibiotic-treated host 40
(following another infection
and treatment with a different 30
antibiotic, e.g. methicillin)
causing multiple-antibiotic-
resistant bacteria to evolve 20
10
overuse and misuse of antibiotics create the 0

perfect breeding ground for resistant bacteria 1992 1994 1996 1998 2000
development of multiple-resistant
In the long term, the drugs industry faces
Staphylococcus aureus, 1992–2001
the challenge of producing new antibiotics
(% of infected samples received in pathology labs)
faster than antibiotic-resistant bacteria evolve.
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Disruptive selection
Disruptive selection occurs when particular environment conditions favour the extremes
of a phenotypic range over intermediate phenotypes. As a result, it is likely that the gene 17
pool will become split into two distinct gene pools. New species may be formed. This
phenomenon has been illustrated by colonisation by plants of mine waste tips (Figure
17.10). These habitats often contain high concentrations of toxic metals such as copper and
lead. Most plants are unable to grow on them. However, you can see from the photograph
that some hardy grasses have colonised the contaminated soil. We can assume that these
species have developed resistance to toxic metal ions. At the same time, their ability to grow

and compete on uncontaminated soils has decreased. In the uncontaminated soil around
the tip, the grasses that have no resistance to toxic metal ions are able to flourish.
Grasses are wind-pollinated plants, so breeding between resistant grass plants and
non-resistant grass plants goes on. When their seeds fall to the ground and attempt to
germinate, disruptive selection may occur. Both the non-resistant plants germinating
on contaminated soil and the resistant plants growing on uncontaminated soil fail to
survive to reproduce. The result is increasing divergence of the populations, initially into
two distinctly different varieties of grass plant. In time, new species may be formed.
disruptive selection
favours two extremes of the ‘chosen’ characters
at the expense of intermediate forms
▲ Figure 17.10 Mining waste tip habitat and disruptive selection
Balancing selection
In directional selection and stabilising selection there is a tendency to reduce variation.
Balancing selection has completely the opposite effect.
Balancing selection is a process which actively maintains multiple alleles in the gene
pool of a population. It does this at frequencies well above that due to gene mutation. An
example of this is sickle cell trait. This is a hereditary condition that causes a proportion
of the red blood cells circulating in the body to be sickle-shaped. You can see a sample
of red blood cells from the circulation of someone with sickle cell trait in Figure 16.27
(page 370). This illustration also explains the mutation by which the gene that codes for
the amino acid sequence of the beta chain of haemoglobin is prone to a substitution of
the base adenine (A) by thiamine (T) in a codon coding for the amino acid glutamic acid.
As a consequence, the amino acid valine appears at that point instead. When the genetic
code of this mutated gene has been transcribed into messenger RNA and then translated
at ribosomes, molecules of an unusual form of haemoglobin, known as haemoglobin Hbs,
results. The molecules with this unusual haemoglobin tend to clump together and form
long fibres that distort the red blood cells into sickle shapes. In this condition the red
blood cells transport little oxygen and they may even block smaller vessels. In people
who are heterozygous for this allele, Hb Hbs, less than 50 per cent of their red blood cells
are sickle-shaped. Sickle cell trait is a non-lethal condition. However, people with it are
mildly anaemic and we might expect them to be at some disadvantage in life. However,
there are areas of the world where this is definitely not so.
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The world distribution of malaria is shown in Figure 10.7 (page 205). This disease kills
a large number of people each year. Notice that in regions of Africa and India malaria
17 is endemic. Here, sickle cell trait confers an advantage. This is because the malarial
parasite Plasmodium completes its lifecycle in red blood cells, but it cannot do so in
red blood cells containing Hbs. So a person who inherits the sickle cell allele from one
parent and the normal haemoglobin allele from the other (a heterozygote) is resistant to
the malarial parasite. However, people who are homozygous for the sickle cell allele
(Hbs Hbs) have sickle cell anaemia and this affects their survival rate.
So we see balancing selection at work here. Turn back to Figure 10.9 (page 207) now and
note the correlation between the distribution of the sickle cell allele and of the distribution of
malaria in Africa.
In any area there are strong selection forces against the homozygous sickle cell
condition; in areas where malaria is endemic there is also a strong selection force
against people homozygous for normal haemoglobin. However, heterozygotes have
a permanent advantage where malaria exists. Heterozygotes are better adapted
than either of the homozygotes. Because of this selective advantage, the sickle-cell
condition is an example of balanced polymorphism – the stable coexistence of two
(or more) distinct types of allele in a species (or population).
Population genetics
Population genetics is the study of genes in populations. Populations are important to
our argument now, because they are where evolution may occur.
A population is a group of individuals of a species, living close together and able to
interbreed. So a population of garden snails might occupy a small part of a garden, say
around a compost heap (Figure 17.11). A population of thrushes might occupy some
gardens and surrounding fields. In other words, the area occupied by a population
depends on the size of the organism and on how mobile it is, for example, as well as on
environmental factors (e.g. food supply, predation). The boundaries of a population may be
hard to define, too. Some populations are fully ‘open’, with individuals moving in or out
from nearby populations. Alternatively, some populations are more or less ‘closed’, that is,
isolated communities, almost completely cut off from neighbours of the same species.
Figure 17.11 The concept

of ‘population’ hedge (home to ‘open’ population of
predators of snails of flower bed
garden snail)
snail migration
limited ‘open’ population
snail of snails, around
migrations compost heap
‘semi-open’ population
‘closed’ population of
of snails in vegetable patch
snails on traffic island
flower bed
roadways
(barrier to effective
migrations of snails in most cases)
Populations and gene pools

In any population, the total of the alleles of the genes located in the reproductive cells of
the individuals make up a gene pool.
When breeding between members of a population occurs, a sample of the alleles of the
gene pool will contribute to form the genomes (gene sets of individuals) of the next
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generation, and so on, from generation to generation. Remember, an allele is one of a
number of alternative forms of a gene that can occupy a given locus on a chromosome.
The frequency with which any particular allele occurs in a given population will vary. 17
When allele frequencies of a particular population are investigated they may turn out
to be static and unchanging. Alternatively, we may find allele frequencies changing.
They might do so quite rapidly with succeeding generations, for example.
When the allele frequencies of a gene pool remain more or less unchanged, then we
know that population is static as regards its inherited characteristics. We can say that
the population is not evolving.

However, if the allele frequencies of gene pool of a population are changing (i.e. the
proportions of particular alleles are altered, we say ‘disturbed’ in some way), then we
may assume that evolution is going on. For example, some alleles may be increasing
in frequency because of an advantage they confer to the individuals carrying them.
With possession of those alleles the organism is more successful. It may produce more
offspring, for example. If we can detect change in a gene pool we may detect evolution
happening, possibly even well before a new species is observed.
How can we detect change or constancy in gene pools?

The answer is, by a mathematical formula called the Hardy–Weinberg principle
(Figure 17.12). Independently this principle was discovered by two people, in the
process of explaining why dominant characteristics don’t take over in populations,
driving out the recessive form of that characteristic. (For example, at that time people
thought [wrongly] that human eye colour was controlled by a single gene, and that
an allele for blue eyes was dominant to the allele for brown eyes. ‘Why doesn‘t the
population become blue-eyed?’, was the issue.)
Let the frequency of the dominant allele (G) be p, and the frequency of the recessive allele (g) be q.
The frequency of alleles must add up to 1, so p + q = 1.
This means in a cross, a proportion (p) of the gametes carries the G allele, and a proportion (q) of the gametes
carries the g allele.
The offspring of each generation are given by the Punnett square.
G G
gamete frequency
p p
g GG g
q p2 q So the progeny are respectively:
Gg Gg p2 = frequency of GG homozygote
pq pq 2pq = frequency of Gg heterozygote
gg q2 = frequency of gg homozygote
q2
Hardy–Weinberg principle
If the frequency of one allele (G) is p, and the frequency of the other allele (g) is q then the frequencies of the three
possible genotypes GG, Gg and gg are respectively p2, 2pq and q2.
In this way, Hardy and Weinberg developed the following equation to describe stable gene pools:
p2 + 2pq + q2 = 1
frequency of frequency of frequency of total
homozygous heterozygous homozygous
dominant individuals recessive
individuals individuals
▲ Figure 17.12 Deriving the Hardy–Weinberg principle
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The main problem of finding gene frequencies is that is not possible to distinguish
between homozygous dominants and heterozygotes based on their appearance or
17 phenotype. However, using the above equation, it is possible to calculate gene frequency
from the number of homozygous recessive individuals in the population. This is q2. We
can find q by finding the square root. The result tells us the frequency of the recessive
allele, and this can then be substituted into the initial equation p 1 q 5 1 and we can
find the frequency of the dominant allele.
Using the Hardy–Weinberg principle

The Hardy–Weinberg principle can be used to find the frequency of a gene in cases of
dominance where we are unable to distinguish between the homozygous dominants and
the heteroygotes on the basis of phenotype.
» Example 1:
In humans, the ability to taste the chemical phenylthiocarbamide (PTC) is
conferred by the dominant allele T. Both the dominant homozygotes (TT) and the
heterozygotes (Tt) are ‘tasters’. The non-tasters are the homozygotes (tt).
In a sample of a local population of 200 people in Western Europe, 130 (65 per cent)
were tasters and 70 (35 per cent) were non-tasters.
Phenotypes Tasters Non-tasters

Genotypes TT + Tt tt
Frequency 0.65 0.35
Apply this data to the Hardy–Weinberg principle; we know the value of q2 to be 0.35.
Taking the square root the value of q 5 0.59.
So the frequency of the non-tasting alleles (t) in this European population was 0.59.
» Example 2:
The absence of the skin pigment, melanin, is a condition called albinism (Figure 16.26,
page 369), a genetically controlled characteristic. An albino has the genotype pp
(homozygous recessive), whereas people with normal pigmentation are homozygous
(PP) or heterozygous (Pp). In a large population, only one person in 10 000 was albino.
From the equation above, homozygous recessives (pp) 5 q2.
Thus q2 5 0.0001, so q 5 √0.0001 5 0.01.
So substituting into the initial equation p 1 q 5 1,
p 1 0.01 5 1, therefore p 5 0.99.
Thus the Hardy–Weinberg principle has allowed us find the frequencies of alleles P
and p in a population.
Incidentally, it has also shown that the frequency of ‘carriers’ of an allele for albinism
in the population (Pp) is quite high (about 1 in 50 of the population) despite the fact
that albinos make up only 1 in 10 000. In other words, very many more people carry
around an allele for albinism than those who know they may do so.
Hardy–Weinberg and ‘disturbing factors’

The Hardy–Weinberg principle predicts that the gene pool in a population does not
change in succeeding generations. That is, genes and genotype frequencies normally
remain constant in a breeding population, provided that:
» the breeding population under investigation is a large one
» there is random mating, with individuals of any genotype all equally likely to mate with
individuals of any other genotype (e.g. no one genotype is being selectively predated)
» there is no introduction of new alleles into the population, either by mutations or by
immigration of new breeding individuals.
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But gene pools do change
In some populations, the composition of the gene pool changes. This may be due
to a range of factors, known as ‘disturbing factors’ in that they operate to alter the 17
proportions of some alleles.
1 Selection
We have already noted various ways in which natural selection operates to change
the composition of gene pools. A further example will suffice here.
Selective predation of members of the population with certain characteristics that
are genetically controlled, will lead to changing frequencies of certain alleles. For

example, selective predation of snails with a particular shell coloration that makes
them visible in (say) a grassland habitat, but effectively camouflaged in a woodland
habitat (Figure 17.13).
the thrush (Turdus ericetorum)
selectively predates local
woodland leaf litter populations of snails, using a
stone as an ‘anvil’ to break the
shell so that it can eat the snail grass
The banded, coloured shells
of the snail Cepea nemoralis
are common sights in woods,
hedges and grasslands. The
shells may be brown, pink
or yellow, and possess up to
five dark bands. In woodland
leaf litter the shells that are
camouflaged are darker and
more banded than those
camouflaged among grasses.
▲ Figure 17.13 Selective predation of snails – natural selection in operation
2 Genetic drift
In a very large breeding population there is every likelihood that the sample of
genes coming together in zygotes will be fully representative of the gene pool, and
so of previous generations, too. On the other hand, in a small population the genes
selected may not be representative of the gene pool as a whole.
In the event of sudden hostile physical conditions, such as extreme cold,
devastating flooding or prolonged drought, a natural population may be reduced
to a very few survivors – this creates a genetic bottleneck. On the return of a
favourable environment, the numbers of the affected species may quickly return
to normal (typically, because of reduced competition for food or other resources).
However, the new population has been built from a very small sample of the
original, ‘pre-disaster’ population, with numerous ‘first cousin’ and backcross
matings (causing fewer heterozygotes and more homozygotes) and with some
alleles lost altogether (Figure 17.14, overleaf).
3 Founder effect
A small group of a large breeding population may become isolated, possibly due to a
barrier that arises within part of the territory, or when a small group wander away,
or are carried away by chance – such as by a tsunami. If these small samples of the
original population are unrepresentative of the original population, a sudden change
in gene frequency will have taken place.
Question
4 Other ‘disturbing factors are:
4 What factors Emigration/immigration. This may introduce new genes into populations, for
may cause the example.
composition of a
Mutation. These are random, rare, spontaneous changes in the genes that occur in
gene pool to change?
gonads, leading to the possibility of new characteristics in the offspring.
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population size
different alleles
17 of a gene
original population
has stable size and
genetic diversity for
many generations
passage of time
population crashes—
the individuals that
survive carry only some
of the alleles present in
the original population
population numbers
recover but genetic
diversity remains low
▲ Figure 17.14 A genetic bottleneck results from a sudden reduction in the size of a
population and causes a reduction in the genetic diversity of that population
17.2 continued…Artificial selection

Learning outcomes
17.2.6 describe the principles of selective breeding (artificial selection)
17.2.7 outline the following examples of selective breeding: the introduction
of disease resistance to varieties of wheat and rice, inbreeding and
hybridisation to produce vigorous, uniform varieties of maize, improving
the milk yield of dairy cattle
Starting point
★ Humans use selective breeding (artificial selection) to improve features in
ornamental plants, crop plants, domesticated animals and livestock.
Question Artificial selection is selection caused by humans. This process of selective breeding
is usually a deliberate and planned process. Artificial selection involves identifying the
5 Charles Darwin largest, the best or the most useful of the progeny for the intended purpose and using
argued that the great them as the next generation of parents. Then, continuous removal of progeny showing
wealth of varieties less desired features, generation by generation, leads to deliberate genetic change. The
we have produced genetic constitution of the population changes rapidly. Artificial selection is an ongoing
in domestication process to obtain higher yields, superior nutrient content and resistance to disease in
supports the concept very many of today’s domestic animals and crop plants.
of evolution. Outline
how this is so. Charles Darwin started breeding pigeons as a result of his interest in variation in
organisms (Figure 17.15). In On the Origin of Species he noted there were more than a
dozen varieties of pigeon which, had they been presented as wild birds to an expert
on birds, would have been recognised as separate species. All these pigeons were
descendents of the rock dove, a common wild bird.
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Darwin argued that if so much change can be induced in so few generations, then
species must be able to evolve into other species by the gradual accumulation of minute
changes, as environmental conditions change and select some progeny and not others. 17
rock dove (Columbia livia)
from which all varieties of
pigeon have been derived

jacobin
fantail
pouter
▲ Figure 17.15 Pigeon varieties produced by selective breeding

Question
By artificial selection, the plants and animals used by humans (such as in agriculture,
6 Explain the key transport, companionship and leisure) have been derived from wild organisms. The
difference between origins of artificial selection go back to the earliest developments of agriculture,
natural and artificial although at this stage, successful practice was not based on an understanding of the
selection.
theory of evolution (Figure 17.16).
The steps to domestication of wild animals

1 A wild population of a ‘species’ useful as a source of hides, meat, etc. is identified and
people learn to distinguish it from related species. Herd animals (such as sheep and
cattle) are naturally sociable and lend themselves to this.
2 Once a wild herd has been trapped inside a compound or field, there is a selective
killing (culling) of the least suitable members of this herd in order to meet immediate
needs for food and materials for living.
3 Breeding is encouraged among members of the herd showing the desired feature and
they are protected from attack by wild predators.
4 From the offspring, the individual with the most useful features is selected and used
as the future breeding stock.
5 The breeding stock is maintained during unfavourable conditions, such as drought
and floods.
6 After a long period of artificial selection, a domesticated herd, dependent on the
herds people rather than living wild, is established. This leads to the possibility of
trading individuals of a breeding stock with other groups of herds people living
nearby who have similar stocks. This introduces a wider gene pool into the herd –
and may introduce fresh characteristics.
Wild sheep or mouflon (Ovis musimon) Soay sheep of the outer Hebrides Modern selective breeding has produced
occur today on Sardinia and Corsica suggest to us what the earliest shorter animals with a woolly fleece in place
domesticated sheep looked like of coarse hair and with muscle of higher fat
content. Many breeds have lost their horns
▲ Figure 17.16 From wild to domesticated species and the origins of selective breeding skills
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Examples of crop improvement by selective breeding
17 Cereal grains are highly significant components of human diet. Plant matter forms
the bulk of human food intake in both developed and less-developed countries, but
it is plants of one family, the grasses, which we and most of our livestock depend on
(Figure 17.17). This family includes cereals, which are the fruits (grain) of cultivated
grass species. They are relatively easy to grow and the mature grains they yield are
comparatively easy to store. Grains contain significant quantities of protein, as well as
starch, as we shall shortly see. Fortunately for some of the huge and growing human
population the Earth is increasingly required to support at this time, sheep and goats
feed mostly on grass leaves, rather than requiring precious grain stocks.
On the other hand, cattle and poultry in the developed world are largely fed on grain
such as maize. Because much arable land is used to grow grain for feeding livestock,
others go hungry. In the USA, 157 million tonnes of cereals, legumes and vegetable
protein (all suitable for human consumption) are fed to livestock to produce just 28
million tonnes of animal protein (meat).
Bangladesh
population > 161 000 000
plant matter in diets = 96% UK
(cereals = 82.1%) population > 62 500 000
plant matter in diets = 63%
(cereals = 21%)
Edible dry
matter
Food crop provided Key
% of diet from cereals
1 Wheat 468
(cultivated grasses)
2 Maize 429
% of diet from
3 Rice 330 other plant matter
4 Barley 160 % of diet from

animal matter
5 Soybean 88
▲ Figure 17.17 Plant matter as a proportion of the human diet
6 Cane 67
sugar
7 Sorghum 60 Actually, the number of plant species that humans depend upon for their food is
8 Potato 54 quite limited – about 300 species out of a total number of flowering plant species
that approaches 200 000. Of these 300 common food plants, just 17 species provide
9 Oats 43
90 per cent of our food. Furthermore, from Table 17.3 you can see that four grain plants
10 Cassava 41 contribute by far the most.
▲ Table 17.3 The world’s So, it is largely the grains of certain cultivated grasses which stand between humans and
top ten food crops and
starvation – to state a fact rather dramatically!
the estimated edible dry
matter (in millions of
tonnes) they provide Disease resistance in varieties of wheat and rice
Plants used in agriculture and horticulture have been obtained by genetic manipulation
of wild plants. Today, new varieties have been developed. There are two ways in which
this is done.
1 Artificial selection
In traditional breeding projects, the most useful offspring for a particular purpose,
such as resistance to specific pest and diseases, are selected and used as the next
generation of parents. Offspring regarded as less useful are excluded. This technique
has been applied with increasing sophistication, and is still in common use by
researchers.
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2 Genetic engineering (recombinant DNA technology)
Today, genetic modification is also achieved by the direct transfer of genes
from one organism to the set of genes (the genome) of another, often unrelated
organism. In green plants, introducing genes into cells is complicated by the
17
presence of the cell wall. However, walls may be temporarily removed by the
gentle action of enzymes, leaving a cell protoplast. Genes may be introduced into
protoplasts, or differing protoplasts induced to fuse together, rather like gametes
do. Alternatively, genetic modification can be brought about by the tumour-
forming bacterium Agrobacterium. The gene for tumour formation occurs in a
plasmid. Useful genes may be added to the plasmid, too. Then, the gall tissue the

bacterium induces in a plant it attacks (and the new plants grown from it) may
contain and express the new gene.
Today, new varieties of wheat and rice have been developed by genetic engineering,
including varieties resistant to diseases. Most plant diseases are caused by fungal
pathogens, and there are naturally synthesised peptides with antimicrobial
properties, the genes for which have been engineered into high-yielding varieties.
This technique is proving a valuable tool in the control of a wide range of fungal
pathogens. The peptides have proved harmless to humans and other animals.
Breeding of vigorous, uniformly growing varieties of maize

Maize is the second most important food crop (Table 17.3). It was probably originally
domesticated in an area we now know as Mexico. Today maize is grown all over the
world, but most intensively in the USA. Modern varieties are hybrids – the original
form of wild maize has long been extinct. Maize has characteristic wind-pollinated
flowers with both male and female flowers on the same plant (Figure 17.18, overleaf).
The male flowers occur at the top (terminally) with pendulous stamens and versatile
anthers. Below are the female flowers (the cobs), in the axils of the leaves. They have
huge, feathery stigma (the tassels). The plant is capable of self-pollination, leading
to self-fertilisation, but naturally tends to cross-pollinate. Self-fertilisation in maize
largely prevented because male and female flowers mature at different times. Maize
lends itself to crossings during controlled plant breeding experiments when adjacent
rows of varieties (possibly previously inbred) are prevented from self-pollinating by
removal of the tassels (‘detasselling’).
Today’s growers and consumers seek in maize the following characteristics:
» plants that grow vigorously in the local environment (climate, soil), but that are
resistant to diseases and that result in high yielding cobs
» crops of fairly standard size (height) and with cobs that are ready to harvest at the
same time, to facilitate harvesting.
Plants originally grown in the wild would have had some of these characteristics, but
not all. Selective breeding has been undertaken over the years to achieve the quality
and consistency required. Remember, consistent inbreeding (producing generations
by self-pollination) leads eventually to plants that lack vigour and fertility and have
reduced size and yield. This is referred to as inbreeding depression. However,
inbreeding does generate plants which show little variation (a standardised crop), for
they will tend to have the same alleles for most genes.
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male flowers female flowers
17
▲ Figure 17.18 A modern maize plant in flower
When inbred lines are crossed the

detasseled detasseled
results are hybrids which exhibit
hybrid vigour – the hybrids show
fro len
D
po m B
m
l
fro
po
lle
greater yields and more vigorous

n
growth. This is because, in them,

fewer recessive alleles are expressed.
However, if cross-fertilisation
continues at random, the results are
crops with much variation between
individual plants.
The most successful breeding
experiments have started with ‘parent’
inbred B inbred A inbred C inbred D
generations which are selectively
single-cross seed detasseled single-cross seed inbred to deliver high yield and
(A × B) produced (C × D) produced other valuable characteristics such
)
×D
in an isolated field in an isolated field as disease resistance (achieved by

fro llen
(C
exposure to the pest and use in

m
po
further breeding programmes only of

those plants which remain pest free).
These parent generations are then
involved in double-cross hybridisation
(Figure 17.19). The result has been
maize fruit that when planted and
cultivated appropriately, produces
crops with spectacularly increased
single-cross single-cross yields, but without the loss of other
plant (A × B) plant (C × D)
favourable characteristics.
double-cross seed (A × B) × (C × D)
is produced in an isolated field, sold to
the farmer, and planted to produced
high-yielding double-cross corn
▲ Figure 17.19 The production of double-cross hybrid corn

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Selective breeding of dairy cattle for improved milk yield
In highly developed agricultural systems, principally the USA and Western Europe, milk
yield per cow has more than doubled in the past 50 years. Holstein Friesian cattle are
17
today’s most productive. This breed originated in Europe, in Holland and Germany, and
proved to be the animals that could best exploit the abundant grass resources available
(Figure 17.20).
EXTENSION
17.3 Evolution
Cows as ruminants:
Cellulose, the most abundant organic compound,
is a major component of the diet of all herbivores.
Mammals are unable to produce the enzyme cellulase,
but many bacteria can. Herbivores exploit this facility of
microorganisms in order to digest the cellulose in their
diet. Cows have a four-chambered ‘stomach’. The first
compartment, the rumen, is a large fermentation tank
containing microorganisms able to digest cellulose.
Digestion of cellulose begins with grinding by jaws
and teeth. Later on, in the cycle of fermentation,
grass is also regurgitated to the mouth from the
rumen for further grinding. Meanwhile, much of the ▲ Figure 17.20 A herd of Holstein cows
sugar released by cellulase during fermentation in
the rumen is turned into organic acids. Sugars and amino acids and proteins from inorganic nitrogen
organic acids are the major source of energy for the (NO3– ions, NH3). When, later, the contents of the
cow, and are absorbed as soon as they are formed. The rumen pass on to the true stomach, the cow digests the
microorganisms present also synthesise their own microorganisms as an additional source of protein.
Many cows now produce more than 20 000 kg of milk per lactation. This has been
achieved by selecting bulls from high-yield herds, and breeding them with cows that
have the best milk production. The use of artificial insemination techniques and the
maintenance of stocks of frozen semen have permitted the use of semen from the most
promising of animals to have the widest impact. However, at the same time there has
been a substantial reduction in fertility in milking herds. Each lactation starts following
the birth of a calf, but first the cow has to be inseminated as the previous lactation
comes to an end. This cycle has started to become problematical in some of the highest
yield cows. Research now indicates there may be a genetic connection, and the problem
is under intensive investigation.
17.3 Evolution
Learning outcomes
17.3.1 outline the theory of evolution as a process leading to the formation of
new species from pre-existing species over time, as a result of changes to
gene pools from generation to generation
17.3.2 discuss how DNA sequence data can show evolutionary relationships
between species
17.3.3 explain how speciation may occur as a result of genetic isolation
by: geographical separation (allopatric speciation), ecological and
behavioural separation (sympatric speciation)
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Starting points
17 ★ Isolating mechanisms can lead to the accumulation of different genetic
information in populations, potentially leading to new species.
★ Over prolonged periods of time, some species have remained virtually
unchanged, others have changed significantly and many have become extinct.
Evolution by natural selection – the ideas and arguments

By evolution we mean the gradual development of life in geological time. The word
evolution is used widely, but in biology it specifically means the processes by which life
has been changed from its earliest beginnings to the diversity of organisms we know about
today, living and extinct. It is the development of new types of living organisms from pre-
existing types by the accumulation of genetic differences over long periods of time.
Charles Darwin (1809–82) was a careful observer and naturalist who made many
discoveries in biology. After attempting to become a doctor (at Edinburgh University)
and then a clergyman (at Cambridge University), he became, in 1831, the unpaid
naturalist on an expedition to the southern hemisphere on a ship called HMS Beagle. On
this five-year expedition around the world and in his later investigations, he developed
the idea of organic evolution by natural selection.
Darwin was very anxious about how the idea of evolution might be received and he
made no moves to publish it until the same idea was presented to him in a letter by
another biologist and traveller, Alfred Russel Wallace. Only then, in 1859, was On the
Origin of Species by Natural Selection completed and published.
The arguments and ideas of On the Origin of Species are summarised in Table 17.4.
Statements/deductions
S1 Organisms produce a far greater number of progeny than ever give rise to
mature individuals.
S2 The number of individuals in species remains more or less constant.
D1 Therefore, there must be a high mortality rate.
S3 The individuals in a species are not all identical, but show variations in their
characteristics.
D2 Therefore, some variants will have more success than others in the
competition for survival. So the parents for the next generation will
be selected from those members of the species better adapted to the
conditions of the environment.
S4 Hereditary resemblance between parents and offspring is a fact.
D3 Therefore, subsequent generations will maintain and improve on the degree
of adaptation of their parents by gradual change.
▲ Table 17.4 Charles Darwin’s ideas about the origin of species, summarised in four
statements (S) and three deductions (D) from these statements
Neo-Darwinism
Charles Darwin (and nearly everyone else in the scientific community of his time) knew
nothing about Mendel’s work on genetics. Chromosomes had not been reported, and the
existence of genes, alleles and DNA were unknown.
Instead, biologists generally subscribed to the concept of ‘blending inheritance’
when mating occurred (which would reduce the genetic variation available for
natural selection).
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Today, modern genetics has shown us that blending generally does not occur and
Questions
that there are several ways by which genetic variation arises in gamete formation
7 Put in your own
words the ideas from
and fertilisation. Neo-Darwinism is a restatement of the ideas of evolution by natural
selection in terms of Mendelian and modern genetics. The ideas of Neo-Darwinism are
17
modern genetics summarised below.
that provide a basis
for the theory of the Genetic variation arises by:
origin of species by » mutations, including chromosome mutations and gene mutations
natural selection. » random assortment of paternal and maternal chromosomes during meiosis, which
occurs in the process of gamete formation
8 Suggest the
17.3 Evolution
» recombination of segments of maternal and paternal homologous chromosomes
significance for the
theory of evolution during crossing over that occurs during meiosis in gamete formation
by natural selection » the random fusion of male and female gametes in sexual reproduction (which was
of the realisation by understood in Darwin’s time).
geologists that the Then, when genetic variation has arisen in organisms:
Earth was more than » it is expressed in their phenotypes
a few thousand years » some phenotypes are better able to survive and reproduce in a particular
old. environment, while others fail to – a point known as ‘differential survival’
» natural selection operates, determining the survivors and the genes that are
perpetuated.
In time, this process may lead to new varieties and new species.
Survival of the fittest?

The operation of natural selection is sometimes summarised in the phrase survival of
the fittest, although these were not words that Darwin used, at least not initially.
Question To avoid the criticism that ‘survival of the fittest’ is a circular phrase (how can fitness
be judged except in terms of survival?), the term ‘fittest’ is understood in a particular
9 Deduce the context. For example, the fittest of the wildebeest of the African savannah (hunted
importance of herbivores) may be those with the acutest senses, quickest reflexes and strongest leg
modern genetics to muscles for efficient escape from predators. By natural selection of these characteristics,
the theory of the the health and survival of wildebeests is assured.
origin of species by
natural selection. Molecular evidence for evolutionary relationships
Evidence from protein sequence data
All living things have DNA as their genetic material, with a genetic code that is virtually
universal. The processes of ‘reading’ the code and protein synthesis, using RNA and
ribosomes, are very similar in prokaryotes and eukaryotes, too. Processes such as
respiration involve the same types of steps and similar or identical intermediates and
biochemical reactions, similarly catalysed. ATP is the universal energy currency. Also,
among the autotrophic organisms the biochemistry of photosynthesis is virtually
identical.
This biochemical commonality suggests a common origin for life, as the biochemical
differences between the living things of today are limited. Some of the earliest events in
the evolution of life must have been biochemical, and the results have been inherited
widely. However, large molecules such as nucleic acids and the proteins they may code
for are subjected to changes with time, but this change may be an aid to the study of
evolution and relatedness. It is possible to measure the relatedness of different groups
of organisms by the amount of difference between specific molecules such as DNA,
proteins and enzyme systems – which is a function of time since particular organisms
shared a common ancestor.
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Variations in haemoglobin molecules that indicate relatedness
17 Haemoglobin, the b chain of which is built from 146 amino acid residues, shows variations
in the sequence of amino acids in different species in which it occurs. Haemoglobin
structure is determined by inherited genes, so the more
Species Differences Species Differences closely related species are, the more likely their amino acids
Human 0 Kangaroo 38 sequence match (Table 17.5). Variations are thought to arise
by mutations of an ‘ancestral’ gene for haemoglobin. If so,
Gorilla 1 Chicken 45
the earlier that species diverged from a common ancestor,
Gibbon 2 Frog 67 the more likely it is that differences may arise.
Rhesus 8 Lamprey 125

Similar studies have been made of the differences in the
monkey
polypeptide chains of other protein molecules, including
Mouse 27 Sea slug (mollusc) 127 ones common to all eukaryotes and prokaryotes. One
such is the universally occurring electron transport
▲ Table 17.5 Number of amino acid differences in b chain of
carrier, cytochrome c.
haemoglobin compared to human haemoglobin
Biochemical variation used as an evolutionary clock

Biochemical changes like these may occur at a constant rate, and if so, may be used as
a ‘molecular clock’. If the rate of change can be reliably estimated, then they do record
the time that has passed between the
Immunological studies are a means of detecting differences in specific proteins of species, separations of evolutionary lines. In the
and therefore (indirectly) their relatedness.
case of the haemoglobin of vertebrate
sample of human serum (blood minus later, sample of rabbit’s blood taken animals the haemoglobin ‘clock’ does
cells and fibrinogens) obtained for anti-human antibodies (rabbit appear to ‘tick’ regularly.
antibodies to human proteins)
Immunological studies are another
human serum means of detecting differences in specific
injected into
rabbit
proteins of species, and therefore
(indirectly) their relatedness. Serum is
a liquid produced from blood samples
from which blood cells and fibrinogen
have been removed. Protein molecules
present in the serum act as antigens if
serum from other mammals the serum is injected into animals with
mixed with anti-human antibodies
an immune system that lacks these
proteins.
the more closely related human anti-human
the animal is to human serum antibodies Typically, a rabbit is used when
the greater the investigating relatedness to humans.
precipitation
The injected serum causes the
production of antibodies against
the injected proteins. Then, serum
produced from the treated rabbit’s
spider anti-human
monkey antibodies
blood (it now contains antibodies
serum against human proteins) can be tested
against serum from a range of animals.
The more closely related the animal is
to humans, the greater the precipitation
observed (Figure 17.21).
pig anti-human The precipitation produced by reaction
serum antibodies
with human serum is taken as 100%.
For each species in Table 17.6, the
greater the precipitation, the more
recently the species shared a common
ancestor with humans.
▲ Figure 17.21 The immune reaction and evolutionary relationships
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This technique, called comparative serology, has been used by taxonomists to establish
phylogenetic links in a number of cases, in both mammals and non-vertebrates.
Difference to Postulated time

17
common ancestor since common
Precipitation Difference from (half difference ancestor (my)
Species (%) human (%) from human) (see below)
Human 100 – – –
Chimpanzee 95 5 2.5 4
17.3 Evolution
Gorilla 95 5 2.5 4
Orang-utan 85 15 7.5 13
Gibbon 82 18 9 15
Baboon 73 27 13.5 23
Spider monkey 60 40 20 34
Lemur 35 65 32.5 55
Dog 25 75 37.5 64
Kangaroo 8 92 46 79
▲ Table 17.6 Relatedness investigated via the immune reaction (my = million years)
We do not know of the common ancestor to these animals and the blood of that
ancestor is not available to test anyway. But if the 584 amino acids that make up blood
albumin change at a constant rate, then the percentage immunological ‘distance’
between humans and any of these animals will be a product of the distances back to the
common ancestor plus the difference ‘forward’ again to any one of the listed animals.
Hence the differences between a listed animal and humans can be halved to gauge the
difference between a modern form and the common ancestor.
Since the radiation of the primates is known from geological and fossil evidence, the
forward rate of change since the lemur gives the rate of the molecular clock – namely
35 per cent in 60 million years (my), or 0.6 per cent every million years. This calculation
can now be applied to all the data (Table 17.6, column 5).
We can now construct a cladogram based on the biochemical data in Table 17.6 –
Figure 17.22.
spider monkey
chimpanzee
orang-utan
kangaroo
baboon
human
gibbon
gorilla
lemur
dog
0
10
time since common ancestor/mya
20
30
40
50
60
70
80
90
▲ Figure 17.22 A cladogram based on immunological evidence in Table 17.6
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DNA hybridisation is a technique that involves matching the DNA Relatedness measured from DNA samples
of different species, to discover how closely they are related.
17 DNA extracted
It is possible to measure the relatedness of different
groups of organisms by the amount of difference
from cells and between specific molecules, such as differences in the
‘cut’ into
fragments,
base sequence of genes in DNA. The genetic differences
about 500 between the DNA of various organisms give us data on
bases long degrees of divergence. Look at Figure 17.23. Here, the
fragments are heated single strands are mixed degree of relatedness of the DNA of primate species
to cause them to with DNA strands from suggests the number of years that have elapsed since
become single strands another species, prepared the various primates shared a common ancestor.
in exactly the same way
(therefore comparable)
Mitochondrial DNA as a molecular clock
DNA has potential as a molecular clock, too. DNA in
eukaryotic cells occurs in chromosomes in the nucleus
base pairing causes the greater the
strands of DNA complementarity (99 per cent) and in the mitochondria. Mitochondrial
to align with of the two strands, DNA (mtDNA) is a circular molecule, very short in
complementary DNA the more bonds link
them together
comparison with nuclear DNA. Cells contain any
number of mitochondria, typically between one
hundred and a thousand.
high complementarity low complementarity

Mitochondrial DNA has approximately 16 500 base
pairs. Mutations occur at a very slow, steady rate in all
DNA, but chromosomal DNA has with it enzymes that
The closeness of the two DNAs is measured by finding may repair the changes in some cases. These enzymes
the temperature at which they separate – the fewer
bonds formed, the lower the temperature required. are absent from mtDNA.
Thus mtDNA changes 5–10 times faster than
The degree of relatedness of the DNA of primate species can be chromosomal DNA – involving about 1–2 base
correlated with the estimated number of years since they shared a changes in every 100 nucleotides per million years.
common ancestor.
Consequently, the length of time since organisms
belonging to different but related species have diverged
p
n
im
bo
bo
can be estimated by extracting and comparing samples

p
ch
gib
gib
him
y
an
of their mtDNA.
on
nk
mo d
on
yc
ng
-ut
rl
mm
wo
n
mm
ma
a
gm
ma
ng
rill
co
Furthermore, at fertilisation, the sperm contributes a

old
sia
ora
py
hu
go
co
0 0
nucleus only (no cytoplasm). All the mitochondria of
1 5 the zygote come from the egg cell. There is no mixing
of mtDNA genes at fertilisation, and so the evidence
2
10 about relationships from studying differences between
difference in DNA /%
samples of mtDNA is easier to interpret in the search for

3
15 early evidence of evolution (Figure 17.24).
mya
4
20
5
25
6
7 30
8 35
▲ Figure 17.23 Genetic difference between DNA samples
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maternal inheritance of mtDNA outer membrane
egg cell
(egg and sperm
not to scale) crista
17
inner membrane
rings of DNA
mitochondria (mtDNA)
17.3 Evolution
with mtDNA
mitochondrion (enlarged)
nucleus with speciation, that is,

DNA of the A two closely related
chromosomes species have
sperm evolved from a
common ancestor
only the sperm
nucleus enters
the egg cell at A1 A2
fertilisation
passage of time
A is one mtDNA *
ring of mtDNA gene (of known
with many base sequence)
genes
*
*
*
chance mutations
accumulate at an
approximately
accumulation of genetic differences in mtDNA
constant rate but at
In mtDNA, mutations involve about 1–2 base changes in every * different locations
100 nucleotides per million years.
*
Studying change in the base pairs of mtDNA genes allows us to detect
evolutionary changes occurring over several hundred thousand years.
*
* random mutations
▲ Figure 17.24 The use of mitochondrial DNA in measuring evolutionary divergence
Speciation
Present-day plants and animals have arisen by change from pre-existing forms of life. This
process has been called ‘descent with modification’ and ‘organic evolution’, but perhaps
speciation is better because it emphasises that species change. So, what is a species?
When Linnaeus devised the binomial system of nomenclature in the 18th century there
was no problem in defining species. It was believed that each species was derived from
the original pair of animals created by God. Since species had been created in this way
they were fixed and unchanging.
In fact the fossil record provides evidence that changes do occur in living things – human
fossils alone illustrate this point. Today, as many different characteristics as possible are
used in order to define and identify a species. The three main characteristics used are:
» morphology and anatomy (external and internal structure)
» cell structure (whether cells are eukaryotic or prokaryotic)
» physiology (blood composition, renal function) and chemical composition
(comparisons of nucleic acids and proteins, and the similarities in proteins between
organisms, for example).
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‘Species’ or ‘variety’?
17 Since species may change (mostly a slow process), there is a time when the differences
between members of a species become great enough to identify separate varieties or
sub-species. Eventually these may become new species.
An illustration of this is the development of tolerance to heavy metal ions in plants able
to survive and even flourish on the otherwise bare mining waste tips commonly found at
sites where ores and minerals have been mined. Here, heavy metals such as zinc, copper,
lead and nickel are often present as ions dissolved in the soil moisture at concentrations
that generate toxic conditions for the plants present on the surrounding unpolluted soils.
We have seen that several heavy metal ions are essential for normal plant growth,
but only in trace amounts. In mining waste these concentrations of ions are
frequently exceeded and heaps left from 18th- and 19th-century mining activities
in several countries around the world remain largely bare of plant cover, even when
surrounding, unpolluted soils have dense vegetation cover. Seeds from these plants
regularly fall on mining waste, but plants fail to establish.
However, careful observations of mining waste at many locations have disclosed the
presence of local populations of plants that have evolved tolerance. One example is the
grass Agrostis tenuis (Bent grass), populations of which are tolerant of otherwise toxic
concentrations of copper (Figure 17.25). Biochemical and physiological mechanisms
have evolved in tolerant species, including:
» the ability to selectively avoid uptake of heavy metal ions
» the accumulation of ions that enter in insoluble compounds in cell walls by the
formation of stable complexes with cell wall polysaccharides
Question
» the transport of toxic ions into the vacuoles of cells, the membrane of which is
10 Explain the unable to pump them out again, so interaction with cell enzymes is avoided.
differences between a
variety and a species. At what point will these copper-resistant forms of Bent grass be recognised as a separate species?
Find out about an The evolution of this form of tolerance has been demonstrated in several species of
example of both from terrestrial plants and also in species of seaweeds tolerant to the copper in the anti-
an organism you are fouling paints frequently applied to the hulls of ships.
familiar with.
Agrostis tenuis (Bent grass)
a common species of poor soils
Experimental investigation of the ability of on hills and mountains
Bent grass plants to grow in the presence
of copper ions at concentrations normally
toxic to plants
140
length of longest root/mm
100
plants from spoil heaps

75 at former copper mine
50
25
plants from
unpolluted soil
0 0.25 0.5 1.0 1.5 2.0
copper in solution/μg cm–3
▲ Figure 17.25 Copper ion tolerance in populations of Bent grass

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Changing gene pools and speciation
A species can have localised populations, although the boundaries of this local
population can be hard to define. Individuals in the local populations tend to resemble 17
each other. They may become quite different from members of other populations.
Local populations are very important because they are potentially a starting point for
speciation. Speciation is the name we give to the process by which one species evolves
into another.
Population genetics is the study of genes in populations. In any population, the total of
the alleles of the genes located in the reproductive cells of the individuals make up a
17.3 Evolution
gene pool. A gene pool consists of all the genes and their different alleles present in an
interbreeding population. When breeding between members of a population occurs, a
sample of the alleles of the gene pool will contribute to form the genomes (gene sets of
individuals) of the next generation, and so on, from generation to generation.
The frequency with which any particular allele occurs in a given population will
vary. By allele frequency we mean how commonly any particular allele occurs in
a population. When allele frequencies of a population are investigated they may
Question turn out to be unchanging. When the allele frequencies of a gene pool remain more
11 What factors or less unchanged, then we know that population is static as regards its inherited
may cause the characteristics. We can say that the population is not evolving.
composition of a Alternatively, allele frequencies may change quite rapidly from generation to generation.
gene pool to change? If the allele frequencies of genes in a population are changing, then we assume that
(Think about the evolution is going on. For example, some alleles may be increasing in frequency because
changes that may go of the advantage they give to the individuals carrying them. Because of these alleles the
on in a population organism is more successful – it may produce more offspring, for example. If we can
and between its detect change in a gene pool we may be seeing evolution happening well before a new
members.) species is observed.
Allopatric speciation: speciation by geographic isolation

A first step to speciation may be when a local population (particularly a small, local
population) becomes completely cut off in some way. Even then, many generations may
elapse before the composition of the gene pool has changed sufficiently to allow us to
call the new individuals a different species. Such changes in local gene pools are an early
indication of speciation.
If a population is suddenly divided by the appearance of a barrier, resulting in two
populations that are isolated from each other, allopatric speciation occurs. Before
separation, individuals shared a common gene pool, but after isolation, ‘disturbing
processes’ such as natural selection, mutation and random genetic drift may occur
independently in both populations, causing them to diverge in their features and
characteristics.
Geographic isolation between populations occurs when natural (or human-imposed)
barriers arise and sharply restrict movement of individuals (and their spores and
gametes, in the case of plants) between the divided populations (see Figure 17.26,
overleaf).
Geographic isolation also arises when motile or mobile species are dispersed to
isolated habitats, as for example when organisms are accidentally rafted from mainland
territories to distant islands. The 2004 tsunami generated examples of this in South
East Asia. Violent events of this type have frequently occurred in the world’s geological
history.
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1 isolation by a new, natural physical barrier
A natural habitat became divided when a river broke
17 its banks and took a new route river
species of forest
plant or animal
later river has formed

a new route
with time, (small) isolated populations of

the species may evolve into separate species
2 isolation by a human-imposed barrier

A new road cuts through established
habitats, separating local populations
▲ Figure 17.26 Geographic barriers
An example of geographical separation leading to speciation has been demonstrated

in the fauna of the Galapagos islands (Figure 17.27). These islands are about 500–600
miles from the South American mainland. The origin of these islands was volcanic; they
appeared out of the sea about 16 million years ago, so we know they were uninhabited,
initially. Today they have flora and fauna that relate to mainland species. There are 10
different species of giant tortoise found on the different islands at the current time.
Shell size and shape vary between the populations. The tortoise species are larger with
domed shells and short necks on the more hilly, humid islands, whereas on islands that
are drier and flatter, the tortoises are smaller with 'saddleback' shells and long necks.
Charles Darwin's observations of these different species of tortoise on the second voyage
of the Beagle in 1835 contributed to his theory of evolution.
Sympatric speciation: speciation by ecological and behavioural

separation
Ecological and behavioural separation occur when members of a local population
come to occupy different parts of a habitat leading to effective separation and therefore
reproductive isolation. An example of sympatric speciation is seen in the terrestrial and
marine giant iguana lizards of the Galapagos islands (Figure 17.28). This giant iguana
lizard had no mammal competition when it arrived on the Galapagos, and it became the
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Many organisms (e.g. insects and birds) may have flown or been carried on wind currents to the
Galapagos from the mainland. Mammals are most unlikely to have survived drifting there on a natural
raft over this distance, but many large reptiles can survive long periods without food or water. 17
immigrant travel to the Galapagos The Galapagos Islands
Today the tortoise population
of each island is distinctive
and identifiable.
17.3 Evolution
Equator
Pinta
Genovesa
Galapagos
Marchena
0°
Santiago
Santa Cruz San Cristóbal

Fernandina
Isabela Santa Fé
1°S
~
Espanola
Floreana
91°W 90°W
▲ Figure 17.27 The Galapagos Islands and species divergence there
The giant iguana lizards on the Galapagos Islands became

dominant vertebrates, and today are two distinct species,
one still terrestrial, the other marine, with webbed feet and
a laterally flattened tail (like the tail fin of a fish).
▲ Figure 17.28 Two distinct species of giant iguana lizards exist on the Galapagos Islands
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dominant form of vertebrate life. Today, two species of iguana lizard are present, one
terrestrial and the other fully adapted to marine life. The latter is assumed to have evolved
17 locally as a result of competition for space and food on the islands (both species are
vegetarian), which drove some members of the population out of the terrestrial habitat.
A further example is the speciation of the North American apple maggot fly, Rhagoletis
pomonella. The fly originally laid its eggs in hawthorn fruit, however, after apple trees
were brought to America by European settlers in the 19th century, some populations
began laying their eggs in apples. Apples mature more quickly than the fruit of
hawthorn trees, so the maggots laid in apples developed sooner than those laid in
hawthorns. Although the populations remain in contact, a temporal separation occurs

due to the difference in the timing of reproductive cycles. This type of speciation is less
common than speciation caused by geographical separation.
Speciation — a summary
Apart from cases of instant speciation by polyploidy, species do not evolve in a
rapid way. The process is usually gradual, taking place over a long period of time.
In fact, speciation may occur over several thousand years, and in all cases requires
‘isolation’.
A deme is the name we give to a small, isolated population. The individuals of a deme are
not exactly alike, but they resemble one another more closely than they resemble members
of other demes. This similarity is to be expected, partly because the members are closely
related genetically (similar genotypes), and partly because they experience the same
environmental conditions (which affect their phenotype).
We have noted above some examples of the ways demes become isolated. Reviewing these,
we see they fall into two groups, depending on the ways isolation is brought about.
» Isolating mechanisms that involve spatial separation are known as allopatric
speciation (meaning literally ‘different country’)
» Isolating mechanisms involving demes in the same location are known as sympatric
speciation (meaning literally ‘same country’).
Allopatric speciation: Sympatric speciation:

due to physical separation of the gene pool due to an isolating mechanism within
by geographic isolation, when motile or a gene pool, preventing production of
mobile species are dispersed to isolated viable offspring between members of
habitats, preventing organisms of related related demes in the same locality due to
demes or their gametes from meeting. behavioural/ecological isolation.
▲ Table 17.7 Comparison of allopatric speciation and sympatric speciation
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SUMMARY
» Evolution is the progressive change in living things breeding population in succeeding generations.
17
in geological time, so that they become better able Disturbing factors that may alter the proportions
to survive in their environment. Evolution occurs of alleles are selective predation, migration,
by natural selection of chance differences. Variation mutation and random genetic drift following a
arises by mutations of genes and chromosomes, dramatic reduction in the size of a population.
by the production of different combinations of » New species may form when a small part of a
alleles that occurs during meiosis as a result of population becomes genetically isolated from

independent assortment and crossing over, and by others by a geographic or reproductive barrier.
the random nature of fertilisation. Alternatively, an abrupt change in the structure or
» A population consists of all the organisms of the number of chromosomes (a chromosome mutation)
same species in a habitat that have the chance may cause an almost instant appearance of a new
to interbreed. A population has the potential to species.
increase in size with little constraint, initially, » Natural selection may work to keep the
but is prevented from doing so indefinitely by characteristics of a species constant (stabilising
environmental factors, which take many different selection), but if the environment changes then
forms. new forms may emerge (directional and disruptive
» The abiotic environment with which organisms selection). Balancing selection is a process which
interact and which may limit the growth of the actively maintains multiple alleles in the gene pool
population includes climatic and soil factors. of a population.
Interactions between organisms of the ecosystem, » Humans have obtained the animals and plants
known as biotic factors, include competition for used in today’s agriculture, transport and leisure
resources and may involve predation, grazing and pursuits by a process of domestication of wild
parasitism. organisms by means of artificial selection.
» The total of all the alleles in a breeding Selective breeding is carried out by careful
population is known as a gene pool. The selection of the parents in breeding crosses
frequency of an allele in a population is known as and the selection of progeny with the required
the allele frequency. In the absence of ‘disturbing features.
factors’ allele frequency does not change in a

1 The Hardy-Weinberg principle may be used to calculate allele and genotype
frequencies for a gene, within a population.
The Hardy-Weinberg principle uses these equations:
p2 + 2pq + q2 = 1
p+q=1
a Within a population of butterflies, the allele for brown wing colour, B, is
dominant to the allele for white wing colour, b.
40% of the butterflies in this population are white.
Use the Hardy-Weinberg principle to calculate the percentage of butterflies in
the population that are heterozygous for the gene controlling wing colour.
Show your working. [3]
b Describe four situations where the Hardy-Weinberg principle does
not apply. [4]
[Total: 7]
(Cambridge International AS and A Level Biology 9700 Paper 42 Q6 Feb/Mar 2017)
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2 Food crops like wheat may be improved by selective breeding and genetic
modification.
17 a Outline how wheat crops have been improved by selective breeding. [4]
b Variation in height of a strain of wheat plants in a field shows a continuous
pattern of variation.
Explain what is meant by continuous variation and explain why this type of
variation occurs in a population. [3]
[Total: 7]
(Cambridge International AS and A Level Biology 9700 Paper 42 Q4 a,b May/June 2016)
3 Spartina species (cord grass) are common plants of estuaries and salt marshes
in many parts of the world. Two species, S. maritima (60 chromosomes – AA
genome) and S. alterniflora (62 chromosomes – BB genome), once grew apart in
different waters of the northern hemisphere. Now they occur together in many
habitats. Today they have been joined by a new species of cord grass, S. angelica
(122 chromosomes – AABB genome). This latter cord grass is a larger plant, and
grows vigorously.
a It is assumed that S. angelica has evolved by a particular mechanism, involving
the other two species. Describe this type of change, how it may have come
about, and the steps that would have been involved. [12]
b Identify another plant species that has evolved by this mechanism. [2]
[Total: 14]
4 a Define the terms ‘gene pool’ and ‘differential mortality’. [2]
b Illustrate what you understand by stabilising selection by means of
an example, and explain the suggestion that stabilising selection does
not lead to evolution. [6]
c What is directional selection? By means of an example, show how
directional selection may lead to new varieties of organism. [6]
d Disruptive or diversifying selection is said to result in balanced
polymorphism. Elaborate this idea by means of a named example and by
specifying the selection forces operating. [6]
[Total: 20]
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A LEVEL
18 Classification, biodiversity and

conservation
18.1 Classification
Classification systems Learning outcomes
attempt to order all the
organisms that exist By the end of this topic, you will be able to:
on Earth according to 18.1.1 discuss the meaning of the term species, limited to the biological species
their characteristics and concept, morphological species concept and ecological species concept
evolutionary relationships 18.1.2 describe the classification of organisms into three domains: Archaea,
with one another. There are Bacteria and Eukarya
opportunities in this topic
18.1.3 state that Archaea and Bacteria are prokaryotes and that there are
for candidates to observe
different species in their
differences between them, limited to differences in membrane lipids,
locality and assess species ribosomal RNA and composition of cell walls
distribution and abundance. 18.1.4 describe the classification of organisms in the Eukarya domain into the
Fieldwork is an important taxonomic hierarchy of kingdom, phylum, class, order, family, genus and
part of a biological species
education because it 18.1.5 outline the characteristic features of the kingdoms Protoctista, Fungi,
provides opportunities to Plantae and Animalia
appreciate and analyse
biodiversity, and to 18.1.6 outline how viruses are classified, limited to the type of nucleic acid (RNA
study the interactions or DNA) and whether this is single stranded or double stranded
between organisms and
their environment. The
biodiversity of the Earth Starting point
is threatened by human
★ Organisms studied locally may be used to show how hierarchical
activities and climate
change. Conserving classification systems are organised.
biodiversity is a difficult
task; individuals, local
groups, national and
international organisations
18.1 Classification
can all make significant
contributions. Candidates
Species – core concepts in environmental study
should appreciate the It was the Swedish botanist Karl Linnaeus (1707–78) who devised the binomial system
threats to biodiversity and of nomenclature in which every organism has a double name consisting of a Latinised
consider some of the steps generic name (genus) and a specific adjective (species). There was no problem in
taken in conservation, both Linnaeus’ day in defining species because it was believed that each species was derived
locally and globally.
from the original pair of animals created by God. Since species had been created in this
way, they were believed to be fixed and unchanging.
In fact, the fossil record provides evidence that changes do occur in living things.
‘Humanoid’ and human fossils alone illustrate this point, as we shall see. Taxonomists
now use as many different characteristics as possible in order to define and identify a
species. The three main characteristics used are:
» external and internal structure (morphology and anatomy)
» cell structure (whether cells are eukaryotic or prokaryotic)
» chemical composition (comparisons of nucleic acids and proteins and the
immunological reactions of organisms).
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A species is a group of organisms of common ancestry that closely resemble each other
structurally and biochemically, and which are members of natural populations that are
18 actually or potentially capable of breeding with each other to produce fertile offspring,
and which do not interbreed with members of other species.
The last part of this definition cannot be applied to self-fertilising populations or to
organisms that reproduce only asexually. Such groups are species because they look very
similar (morphologically similar), and because they behave and respond in similar ways,
with bodies that function similarly (they are physiologically similar).
But however we define the term, since species may change with time (mostly a slow
18 CLASSIFICATION, BIODIVERSITY AND CONSERVATION
process), there is a time when the differences between members of a species become
significant enough to identify separate varieties or sub-species. Eventually these may
become new species. All these points are a matter of judgment.
On a day-by-day basis, biologists frequently use the term ‘species’ when they refer to an
organism they are studying, within the context of a particular aspect of its biology. For
example:
» ecologists refer to species as defined by their ecological niche and how they interact
with the living and non-living parts of their environment
» geneticists refer to species as part of a population whose members have the potential
to interbreed and produce viable fertile offspring
» morphologists refer to species as defined by common body shape and other
structural features by which they are distinguished
» taxonomists refer to species as the smallest group of individuals that share a
common ancestor – a single ‘branch of the tree of life’.
Domains and kingdoms

At one time the living world seemed to divide naturally into two kingdoms consisting of
the plants (with autotrophic nutrition) and the animals (with heterotrophic nutrition).
These two kingdoms grew from the original disciplines of biology, namely botany, the
study of plants, and zoology, the study of animals. Fungi and microorganisms were
conveniently ‘added’ to botany! Initially there was only one problem; fungi possessed
the typically ‘animal’ heterotrophic nutrition but were ‘plant-like’ in structure.
The ‘five kingdoms’ concept

Then, with the use of the electron microscope came the discovery of the two types of
cell structure, namely prokaryotic and eukaryotic (page 23). As a result, the bacteria
with their prokaryotic cells could no longer be ‘plants’ since plants have eukaryotic
cells. The divisions of living things into kingdoms needed overhauling. This led to the
division of living things into five kingdoms.
Table 18.1 The five

Prokaryotae The prokaryote kingdom, the bacteria and cyanobacteria (photosynthetic
kingdoms
bacteria), predominately unicellular organisms
Protoctista The protoctistan kingdom, (eukaryotes), predominately unicellular, and
seen as resembling the ancestors of the fungi, plants and animals
Fungi The fungal kingdom, (eukaryotes), predominately multicellular organisms,
non-motile, and with heterotrophic nutrition
Plantae The plant kingdom, (eukaryotes), multicellular organisms, non-motile,
with autotrophic nutrition
Animalia The animal kingdom, (eukaryotes), multicellular organisms, motile, with
heterotrophic nutrition
Note that viruses are not classified as living organisms – see page 425.
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Extremophiles and the recognition of ‘domains’
Then came the discovery of the distinctive biochemistry of the bacteria found in
extremely hostile environments (the extremophiles – initially, the ‘heat-loving’ bacteria 18
found in hot-springs at about 70°C).
Halophytes – ‘salt-loving’ bacteria Common in salt lakes and where sea water becomes trapped and concentrated
by evaporation where salt has crystallised
Alkalinophiles – ‘alkali-loving’ bacteria Survive at above pH 10, conditions typical of soda lakes
Acidophiles – ‘acid-loving’ bacteria Bacteria of extremely acidic conditions
18.1 Classification
Thermophiles – ‘heat-loving’ bacteria Occur in hot-springs at about 70°C. Some are adapted as to survive at
temperatures of 100–115°C (hyperthermophilic prokaryotes)
Cryophiles – bacteria of sub-zero Common at temperatures of −10°C, as in the ice of the poles where salt
temperatures depresses the freezing point of water
▲ Table 18.2 The range of extremophiles
Since these names were first used, these organisms have been found in a broader range
of habitats. For example, some occur in the oceans, and some in fossil-fuel deposits
deep underground. Some species occur only in anaerobic environments such as the guts
of termites and of cattle, and at the bottom of ponds among the rotting plant remains.
Here they break down organic matter and release methane – with very important
environmental consequences.
Technophiles are different

These microorganisms of extreme habitats have cells that we can identify as ‘prokaryotic’.
However, the larger RNA molecules present in the ribosomes of extremophiles are
different from those of previously known bacteria. Further analyses of their biochemistry
in comparison with that of other groups has suggested new evolutionary relationships.
This discovery led to a new scheme of classification (Figure 18.1, overleaf).
All organisms are now classified into three domains

As a result, we now recognise three major forms of life, called domains. The organisms
of each domain share a distinctive, unique pattern of ribosomal RNA, and there are
other differences that establish their evolutionary relationships (Table 18.3). These
domains are:
» the Archaea (the extremophile prokaryotes)
» the Bacteria (the true prokaryotic bacteria)
» the Eukaryota (all eukaryotic cells – the protoctista, fungi, plants and animals).
This major advance, the recognition that the Archaea were a separate line of
evolutionary descent from bacteria, was made by Carl Woese in 1977. You can read
about him if you put his name into a search engine.
Domains
Biochemical features Archaea Bacteria Eukaryota
DNA of chromosome(s) Circular genome Circular genome Chromosomes
1 Bound protein (histone) present Present Absent Present
2 Introns Typically absent Typically absent Frequent
Ribosomal RNA 70S ribosomes 70S ribosomes 80S ribosomes
Cell wall Present – not made of Present – made of Sometimes present – never
peptidoglycan peptidoglycan made of peptidoglycan
Lipids of cell membrane bilayer Archaeal membranes contain lipids that differ from those of bacteria and eukaryotes
(Figure 18.2, overleaf).
▲ Table 18.3 Biochemical differences between the domains
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The classification of living organisms into three domains on the basis of their ribosomal RNA
These evolutionary relationships have been established by comparing the sequence
18 of bases (nucleotides) in the ribosomal RNA (rRNA) present in species of each group.
animals
Archaea Eukarya
(archaebacteria) fungi (eukaryotes)
Bacteria
(eubacteria) plants
*
*
* The shortest branches lead to hyperthermophilic species which suggests that the
universal ancestor of all living things was a hyperthermophile (possibly ‘assembled’
under conditions at deep ocean vents where volcanic gases are discharged into water
universal at high temperature and pressure).
ancestor?
▲ Figure 18.1 Ribosomal RNA and the discovery of Archaea. Archaea were discovered among prokaryotes of extreme
and inaccessible habitats: subsequently, other members of the Archaea were found more widely – in the gut of
herbivores and at the bottom of lakes and mountain bogs, for example
Phospholipids of bacteria
Phospholipids of archaeal membranes and eukaryote membranes
phosphate group
hydrocarbon tails D-glycerol
L-glycerol
hydrocarbon tails O
–
– unbranched O
– branched H2C –
C O CH2
O P O
C O C H O C O C O–
C O CH2 O H 2C O P O–
ester linkage O
ether linkage
phosphate group
▲ Figure 18.2 The lipid structure of cell membranes in the three domains
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Taxonomy – the classification of diversity
Classification is essential to biology because there are too many different organisms to
sort out and compare unless they are organised into manageable categories. Biological 18
classification schemes are the invention of biologists, based upon the best evidence
available at the time. With an effective classification system in use, it is easier to organise
our ideas about organisms and make generalisations.
The science of classification is called taxonomy. The word comes from taxa (singular:
taxon), which is the general name for groups or categories within a classification
system. The scheme of classification has to be flexible, allowing newly discovered living
18.1 Classification
organisms to be added where they fit best. It should also include fossils, since we believe
living and extinct species are related.
The process of classification involves:
» giving every organism an agreed name
» imposing a scheme upon the diversity of living things.
The binomial system of naming

Many organisms have local names, but these often differ from locality to locality
around the world, so they do not allow observers to be confident they are talking
about the same thing. For example, the name magpie represents entirely different birds
commonly seen in Europe, in Asia and in Sri Lanka (Figure 18.3). Instead, scientists
use an international approach called the binomial system (meaning ‘a two-part
name’). By this system everyone everywhere knows exactly which organism is being
referred to.
European magpie (Pica pica) Asian magpie (Platysmurus leucopterus) Sri Lankan magpie (Urocissa ornate)
▲ Figure 18.3 ‘Magpie’ species of the world
So, each organism is given a scientific name consisting of two words in Latin. The first (a
noun) designates the genus, the second (an adjective) the species. The generic name comes
first, and begins with a capital letter, followed by the specific name. By convention, this name
is written in italics (or is underlined). As shown in Figure 18.4, closely related organisms have
the same generic name; only their species names differ. You will see that when organisms
are frequently referred to, the full name is given initially, but thereafter the generic name is
shortened to the first (capital) letter. Thus, for example, in continuing references to humans
in an article or scientific paper, Homo sapiens would become H. sapiens.
Question 1 In Figure 18.5, overleaf, two animal species are classified from kingdom to species
level. Suggest how this flow diagram needs to be modified to show its classification
from ‘domain’ level.
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Panthera pardus (leopard) Panthera leo (lion) Panthera tigris (tiger)
18
▲ Figure 18.4 Naming organisms using the binomial system – generic name (noun) + specific name (adjective)
+ common name
Question Classification of organisms in the Eukarya domain

In classification, the aim is to use as many characteristics as possible in placing similar
2 Scientific names organisms together and dissimilar ones apart. Just as similar species are grouped
of organisms are together into the same genus (plural: genera), so too, similar genera are grouped together
often difficult to into families. This approach is extended from families to orders, then classes, phyla
pronounce and to and kingdoms. This is the hierarchical scheme of classification; each successive group
remember. Explain containing more and more different kinds of organism. The taxa used in taxonomy are
why they are used. given in Figure 18.5.
Kingdom: Plantae kingdom the largest and most inclusive Kingdom: Animalia
grouping, e.g. plants, animals, fungi, etc.
other phyla other phyla
Phylum: Angiospermophyta phylum organisms constructed Phylum: Chordata

on a similar plan
other classes other classes
Class: Dicotyledonae class a grouping of orders Class: Mammalia

within a phylum
other orders other orders
Order: Fagales order a group of apparently Order: Primates

related families
other families other families
Family: Fagaceae family a group of apparently Family: Hominidae

related genera Normally several species occur
other genera in one genus, many genera make
a family, several families make an
order, and so on. However, this
family contains only one genus.
Genus: Quercus genus a group of similar and Genus: Homo
closely related species
other species
Species: robur species a group of organisms Species: sapiens erectus habilis

‘common oak’ capable of interbreeding to produce ‘modern ‘upright human’ ‘handy human’
fertile offspring human’
extinct species – we learn about
▲ Figure 18.5 The taxa them from fossil evidence only
used in taxonomy and
(a mnemonic to remember the hierarchy of taxa:
applied to two different
King Peter Called Out For Genuine Scientists)
kingdoms
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The characteristic features of the kingdoms Protoctista,
Fungi, Plantae and Animalia 18
The kingdom Protoctista
Includes the algae (including the multicellular seaweeds), the protozoa and the slime
moulds.
Characteristics of the Protoctista:
» Single-celled organisms, or if multicellular, not differentiated into tissues.
18.1 Classification
» Cells are eukaryotic, with a distinct nucleus and membrane-bound organelles.
» Nucleus contains linear chromosomes of DNA with histone protein attached.
» Large ribosomes (80S) present.
» Some protoctista have cell walls, but in others these are absent.
» Nutrition is heterotrophic (in protozoa and slime moulds) or autotrophic (algae).
Amoeba proteus (×200) – a single-celled animal-like organism Chlamydomonas, a motile unicellular alga
of pondwater (×1600)
flagella
cytoplasm
light-sensitive
spot chloroplast
nucleus
cytoplasm
starch storage
endoplasm clear ectoplasm
pseudopodia cell surface

membrane
contractile
vacuole
Fucus, a brown seaweed (×0.5)
nucleus plant body of:
• holdfast (attaches plant
to rock/breakwater)
• stalk
• blade or thallus
food vacuoles midrib
Paramecium
dichotomous
branching
tip may be
swollen with
reproductive
structures
Another alga is Spirogyra
▲ Figure 18.6 The Protoctista

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The kingdom Fungi
18 Includes the moulds, yeasts, mildews, mushrooms and bracket fungi.

The characteristics of the Fungi:
» Multicellular organisms (except the unicellular yeasts), not differentiated into tissues
and non-motile.
» Nucelus contains linear chromosomes of DNA with histone protein attached.
» Cell walls are of chitin.
» Nutrition is heterotrophic.
» Body is made of branching, tube-like hyphae, often dividied by cross-walls into
multinucleate sections.
» Reproduce by spores, produced by asexual and sexual processes.
Yeast feed on sugar solutions, Fungal spores ‘germinate’ quickly

False-colour SEM of yeast wherever they occur. when they land on a suitable
cell budding (×4500) medium under favourable
growing conditions.
mycelium of
Mould fungi hyphae
feed on exposed,
original spore
moist organic
matter.
hyphal tip absorbs nutrients
hyphae and fungal

fruiting bodies on
the surface of the
dung of herbivores
Coprinus (×0.25)
spores dispersed
by flies
typical succession
of fungi
Forest trees live in mutualistic association (both organisms

benefit) with soil-inhabiting fungi. The fungal hyphae that
permeate the soil for a wide area around the tree roots are
continuous with those of the compact sheath around the large bracket fungus
roots. This sheath is the site of exchange of nutrients. releasing spores
a mushroom forms and releases

spores Other fungi feed on
tree tissues, some
parasitically but
others on dead
tissues.
▲ Figure 18.7 The Fungi

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The kingdom Plantae
Includes the mosses, ferns, conifers and flowering plants (broad-leaved trees,
herbaceous plants, leguminous plants and grasses). 18
Characteristics of the Plantae:
» Multicellular organisms, differentiated into tissues; they are non-motile organisms
(but the male gametes of mosses and ferns are motile).
18.1 Classification
» Nutrition is autotrophic.
» Cell walls are largely of cellulose.
Plants that reproduce by spores

Mosses Ferns
– simple plants restricted to damp places – with stem, leaves and roots
– without vascular tissue (xylem and – adapted to terrestrial life
phloem) – vascular tissue present
– without true roots – spores produced on the underside of leaves
– spores produced in a capsule
Flowering plants
– reproduce by seeds
– may be herbaceous or woody
– with stem, leaves and roots with efficient vascular tissue
– stomata in the leaves
– have either broad leaves with net veins or narrow leaves with parallel veins
Broad-leaved plants Narrow-leaves plant (grass)

French bean plant
– plant of the pea and bean family Sugar cane
– found in Europe, Western Asia and – originally from India
Ebony tree North-West Africa – now cultivated widely
– a tropical tree of India – now cultivated widely – commercial source of sucrose
▲ Figure 18.8 The Plantae
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The kingdom Animalia
18 Includes the non-vertebrates, such as worms and arthropods (which includes the
insects), and the vertebrates, which are fish, amphibians, reptiles, birds and mammals.
Characteristics of the Animalia:
» Multicellular organisms, differentiated into tissues; many are motile organisms.
»
Cells sometimes have ciliar or flagella.

» Nutrition is heterotrophic.
» Cell walls are absent.
Non-vertebrate animals
e.g. jellyfish, sea anemones and corals e.g. segmented worms

- marine animals - body of fixed number of
- two layered body walls segments visible externally as rings
- use stinging cells to trap prey - muscular body wall works against
- the corals are important reef-builders hydrostatic (fluid) skeleton
starfish
worm
e.g. flatworms e.g. starfish
- free living flatworms, - predatory marine animals
parasitic flukes and tapeworms of the sea bed
- body three-layered
coral
tapeworm
dragonfly
millipede ant
snail clam
e.g. molluscs spider
- slugs and snails, and
e.g.arthropods
octupuses and clams
lobster - body covered by hard skeleton
- compact bodies with
- have jointed limbs
lungs or gills and a
- spiders, crustaceans, centipedes, millipedes and insects
blood circulation
Vertebrate animals
mammals
- body covered by hair
- have four pentadactyl limbs
- fertilisation and development internal
trout snake - young fed on milk
fish reptiles
- aquatic animals - terrestrial animals with dry, scaly skin
- gas exchange via gills - fertilization internal,
- fertilised eggs laid and
development is external
whale wolf
birds
- body covered
tree frog by feathers
- typically adapted shrew
for fight
amphibians
- terrestial animals partly
adapted to life on land ostrich bear monkey
▲ Figure 18.9 The Animalia
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EXTENSION
Possible evolutionary relationships
18
between the five kingdoms ? = origin of life
A new grouping within archaeobacteria

the prokaryotes is now
recognised – bacteria
that survive under Prokaryotae
extreme conditions bacteria + cyanobacteria
(extremophiles).
18.1 Classification
eukaryotes
The cells of these The cells of these
organisms contain protozoans slime organisms contain
mitochondria. moulds chloroplasts also.
red brown
algae green algae
sponges algae Protoctista
cnidarians
flatworms Fungi
mosses
round
worms ferns
chordates
(= fishes, amphibians,
molluscs
reptiles, birds conifers
and mammals) annelids
flowering plants
arthropods
Animalia Plantae
▲ Figure 18.10 Possible evolutionary relationship between the five kingdoms
Introducing the viruses

Viruses are disease-causing agents that are inactive outside a host cell. They are an
assembly of complex molecules, rather than a form of life. Isolated from their host cell
they are best described as ‘crystalline’. Within susceptible host cells, however, they
are highly active genetic programmes that take over the biochemical machinery of the
host. Here, the component chemicals of the virus are synthesised, and then assembled
to form new viruses. On breakdown (lysis) of the host cell, viruses are released, and
may cause fresh infections. So, viruses are not living organisms, but may become active
components of host cells. For these reasons, viruses are not included in the ‘three
domains’ classification. Remember, antibiotics are ineffective against viruses.
Characteristics of viruses
Viruses are disease-causing agents, rather than ‘organisms’. The distinctive features of
viruses are:
» They are not cellular structures, but rather consist of a core of nucleic acid – either
DNA or RNA – surrounded by a protein coat, called a capsid.
» In some viruses there is an additional external envelope of membrane made of lipids
and proteins, as in HIV (Figure 10.15, page 212) and the influenza virus.
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DNA viruses RNA viruses » They are extremely small when compared with
1 single-stranded DNA: 1 single-stranded RNA: size: 25 nm bacteria. Most viruses are in a size range of
18
‘M13’ virus of poliovirus
bacterial hosts of animal hosts 20–400 nm (0.02–0.4 μm). They are visible only by
retrovirus – means of the electron microscope.
size: 500 nm
human » They can reproduce only within specific living
immunodeficiency
virus of animal hosts cells, so viruses function as endoparasites in their
size: 100 nm host organism.
» They have to be transported in some way between
2 double-stranded DNA: 2 double-stranded RNA:
herpes simplex virus reovirus of hosts.
» Viruses are highly specific to particular host
of animal hosts animal hosts

species, some to plant species, some to animal
species and some to bacteria.
size: 80 nm
» Viruses are classified by whether they contain
size: 200 nm single-stranded DNA (ssDNA), double-stranded
DNA (dsDNA), single-stranded RNA (ssRNA) or
▲ Figure 18.11 The classification of viruses double-stranded RNA (dsRNA) (Figure 18.11).
18.2 Biodiversity
Learning outcomes
18.2.1 define the terms ecosystem and niche
18.2.2 explain that biodiversity can be assessed at different levels, including:
the number and range of different ecosystems and habitats, the number
of species and their relative abundance, the genetic variation within each
species
18.2.3 explain the importance of random sampling in determining the
biodiversity of an area
18.2.4 describe and use suitable methods to assess the distribution and
abundance of organisms in an area, limited to frame quadrats, line
transects, belt transects and mark-release-recapture using the Lincoln
index (the formula for the Lincoln index will be provided, as shown in the
Mathematical requirements)
18.2.5 use Spearman’s rank correlation and Pearson’s linear correlation to
analyse the relationships between two variables, including how biotic
and abiotic factors affect the distribution and abundance of species
(the formulae for these correlations will be provided, as shown in the
18.2.6 use Simpson’s index of diversity (D) to calculate the biodiversity of an
area, and state the significance of different values of D (the formula
for Simpson’s index of diversity will be provided, as shown in the
Starting point
★ Biodiversity is much more than a list of all the species in a particular area.
Ecosystem and niche – core concepts in environmental study

Ecosystem
One of the ideas that ecologists have introduced is that of the ecosystem. This is
defined as a community of organisms and their surroundings, the environment in which
they live and with which they live (Figure 18.12). An ecosystem is a basic functional
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unit of ecology since the organisms that make up a community cannot realistically be
considered separate from their physical environment.
ENERGY FROM SUNLIGHT submerged stems provide

18
rooted plants
a microhabitat for algae
green plants floating plants growing on them
are producers
plankton
18.2 Biodiversity
herbivores
eat plants reed swamp
of margin
carnivores open
eat animals surface
Question water
detrivores eat dead
organic matter mud deposited
3 Name one ecosystem
on pond bottom
in your locality that
decomposers on niche of detritus-feeding
you might study and fish on pond bottom
surface of mud
then list three abiotic
factors affecting consumers
sediment containing examples of habitats
living things in that nutrient reserve
ecosystem.
▲ Figure 18.12 An example of an ecosystem – a lake
Niche
The niche is an ecological term that defines just how an organism feeds, where it lives
and how it behaves in relation to other organisms in its habitat. The niche concept is
useful because it identifies precise conditions which a species needs.
The principle of distinct niches can be illustrated by the two common and rather similar
sea birds, the shag and the cormorant (Figure 18.13). These birds live and feed along the
shag (Phalacrocorax aristotelis) cormorant (P. carbo)
diet is a key difference in the niches of these otherwise similar birds
% of prey taken by
prey shag cormorant
sand eels 33 0
surface-swimming prey
herring 49 1
flatfish 1 26
bottom-feeding prey shrimps, 2 33
prawns
▲ Figure 18.13 Different niches of the shag and the cormorant

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coastline and they rear their young on cliffs and rock systems. We can see they share
the same habitat but their diets and behaviour differ. The cormorant feeds close to the
18 shore on seabed fish, such as flatfish. The shag builds its nest on much narrower cliff
ledges. It also feeds further out to sea and captures fish and eels from the upper layers
of the water. Since these birds feed differently and have different behaviour patterns,
although they occur in close proximity, they avoid competition. Competition refers to
the interaction between two organisms striving for the same resource. For competing
organisms, the more their niches overlap, the more that both will strive to secure a finite
resource. Hence many potential competitors have evolved different niches.
Habitat
The habitat is the locality in which an organism occurs. It is where the organism is
normally found (Figure 18.14). It is easy to give the habitat of some organisms, for
instance the red squirrel is restricted to large blocks of coniferous forest in northern
Asia and Europe. The seaweed bladder wrack is found only in the mid zone of the tidal
seashore. On the other hand, the dandelion occurs widely – on a range of soils but also
in crevices of walls and between paving stones.
If the area of the habitat is extremely small we call it a microhabitat. The insects that
inhabit the crevices in the bark of a tree are in their own microhabitat. Conditions in a
microhabitat are likely to be very different from conditions in the surrounding habitat.
▲ Figure 18.14 The habitats of bladder wrack and the dandelion
Population
By population we mean all the living things of the same species in a habitat at any one
time. The members of a population have the chance of interbreeding, assuming the
species concerned reproduces sexually. All the genes and their different alleles present
in an interbreeding population is called the gene pool. The boundaries of populations of
aquatic organisms occurring in a small pond are clearly limited by the boundary of the
pond. The populations of the garden snail may be found in contrasting habitats. Some
snails occur in extensive and ill-defined areas, around a compost heap, for example,
while others occur in small restricted areas. Meanwhile, a songbird predator of the snail,
the thrush, might occupy the whole garden and its surrounding fields and hedgerows.
In other words, the area occupied by a population depends on the size of the organism
and on how mobile it is, for example, as well as on environmental factors, such as food
supply and predation.
So the boundaries of a population may be hard to define. Some populations are fully
‘open’, with individuals moving in or out from nearby populations. Alternatively, some
populations are more or less ‘closed’, that is, isolated communities almost completely cut
off from neighbours of the same species.
Figure 17.11, on page 392, describes the concept of ‘population’. Look back at it now.
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Community
A community consists of all the living things in a habitat, the total of all the
populations, in fact. So, for example, the community of a well-stocked pond would
18
include the populations of rooted, floating and submerged plants, the populations of
bottom-living animals, the populations of fish and non-vertebrates of the open water
and the populations of surface-living organisms – typically a very large number of
organisms.
Within any community there exists complex interactions between individuals –
Question
18.2 Biodiversity
necessarily, organisms affect each other. This is because the resources required by plants
and animals are in limited supply. Competitive interactions occur between members
4 Use the terms below
of the same species (intraspecific competition) and between members of different
to describe one or
species (interspecific competition). We will revisit aspects of these interactions when
more of the features
we discuss food chains and food webs, energy transfer between trophic levels and the
of a freshwater lake
listed a–g. cycling of nutrients within the environment.
population,
ecosystem, habitat, Introducing biodiversity
abiotic factor, There are vast numbers of living things in the world. The word biodiversity, which
community, refers to this, is a contraction of ‘biological diversity’. It is a term we may use in three
biomass different ways.
a The whole lake
b All the frogs of 1 Biodiversity – the number of species and their relative abundance
the lake Up to now, about 1.7 million species have been described and named. However, until
c The flow of water very recently there has been no attempt to produce an international ‘library of living
through the lake things’ where new discoveries are automatically checked (see below). Consequently,
d All the plants and some known organisms may have been ‘discovered’ more than once.
animals present
Meanwhile, previously unknown species are being discovered all the time. In the UK
e The mud of the alone, several hundred new species have been described in the past decade. We might
lake have expected all the wildlife in these islands to be known, since Britain was one of the
f The temperature countries to pioneer the systematic study of plants and animals. Apparently, this is not
variations in the the case; previously unknown organisms are still frequently found here.
lake
Worldwide, the number of unknown species is estimated at between 3 and 5 million at
g The total mass
the very least, and possibly as high as 100 million. So scientists are not certain just how
of vegetation
many different types of organisms exist. Figure 18.15 overleaf is a representation of the
growing in the
lake. proportions of known and unknown species estimated to exist in many of the major
divisions of living things.
EXTENSION
The Species 2000 Programme
The Species 2000 programme is part of a federation of databases and the
organisations that are creating them, and was set up in 1994. It has the goal of
creating a valid checklist of all of the world’s species of plants, animals, fungi and
microorganisms. This huge task is to be achieved by bringing together existing
species databases covering each of the major groups of organisms. The UK arm
of this initiative is based at the University of Reading. There, Species 2000 is in
partnership with the Integrated Taxonomic Information System (ITIS) of North
America, currently producing the Catalogue of Life, which is linked to the Global
Biodiversity Information Facility (GBIF). You can keep up to date with developments
at www.sp2000.org.
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‘higher plants’,
fungi – mainly the
18 flowering plants
protoctista insects (a class

of the arthropods)
Of the 1.7 million described species,

more than 50% are insects, and the
higher plants, mostly flowering plants,

are the next largest group. By
contrast, only 4000 species of
mammals are known, about 0.25%
other groups of
of all known species. other arthropods
non-vertebrates
(segmented animals
vertebrates with an external
– fish, amphibians, skeleton and jointed
reptiles, birds and limbs)
mammals
▲ Figure 18.15 The relative number of animal and plant groups
2 Biodiversity – the number and range of different ecosystems

and habitats
Ecosystems or habitats are units or components of the living world that we might choose
to study. The biotic element present is likely to contain a huge community of organisms –
the flora, fauna, and microorganisms that occur there. We may also refer to this specific,
localised range of different organisms as ‘biodiversity’.
3 Biodiversity – the genetic variation within each species

The gene pool that the members of each population represent is also referred to as an
aspect of ‘biodiversity’. We will return to this point later, when discussing the reasons
why conservation of biodiversity is important.
Investigating aspects of biodiversity

In the study of a habitat it may be important to collect accurate information on the
size of populations present. A total count of all the members of a population is called
a census. However, such an approach is usually totally impractical because of the size
of the habitat, the movement of animals, and the huge numbers of organisms usually
involved.
For practical reasons it is a random sample that is selected for this, involving either a
part of the area of the habitat, or a restricted number of the whole population. By means
of random sampling, every individual of the population has an equal chance of being
selected, and so a representative sample is assured (Figure 18.16).
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100
90
1 A map of the habitat (e.g. meadowland) is
marked out with gridlines along two edges
80 18
of the area to be analysed. 70
60
y axis
50
40
30
20
18.2 Biodiversity
10
2 Coordinates for placing quadrats are
obtained as sequences of random numbers, 0 10 20 30 40 50 60 70 80 90 100
x axis
using computer software, or a calculator,
or published tables. 100
90
80
70
60
y axis
50
40
3 Within each quadrat, the individual species
30
are identified, and then the density,
frequency, cover or abundance of each 20
species is estimated (Figure 18.17). 10
0 10 20 30 40 50 60 70 80 90 100
x axis
4 Density, frequency, cover, or abundance

estimates are then quantified by measuring
the total area of the habitat (the area
occupied by the population) in square metres.
The mean density, frequency, cover or
abundance can be calculated, using the
equation:
mean density (etc.) per quadrat × total area
population size =
area of each quadrat
▲ Figure 18.16 Random locating of quadrats
Random sampling of plant populations using quadrats

Quadrats are commonly used to estimate plant populations (Figure 18.17, overleaf).
A quadrat is a square frame that outlines a known area for the purpose of sampling.
The choice of size of quadrat varies depending upon the size of the individuals of the
population being analysed. For example, a 10 cm² quadrat is ideal for assessing epiphytic
Pleurococcus, a single-celled alga, commonly found growing on damp walls and tree
trunks. Alternatively, a 1 m² quadrat is far more useful for analysing the size of two
herbaceous plant populations observed in grassland, or of the earthworms and the slugs
that can be extracted from between the plants or from the soil below.
Quadrats are placed according to random numbers after the area has been divided
into a grid of numbered sampling squares (Figure 18.16). The different plant species
present in the quadrat may be identified. Then, using the quadrat an observer may
estimate the density, frequency, abundance or cover of plant species in a habitat. The
steps are outlined in Figure 18.17, including the issue of how many quadrats may need
to be placed for an accurate assessment of population size. An area of chalk grassland is
illustrated in which the use of quadrats would give estimates of the population sizes of
two species of flowering plants.
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Use of the quadrat:
• positioned at random within habitat being investigated
18 • different species present are then identified

• without destroying the plants and the microhabitats beneath
them, plant species’ density, frequency, abundance or cover can be estimated.
density = mean numbers of individuals of each species per unit area (time-consuming
and may be hard to assess separate individuals)
frequency = number of quadrats in which a species occurs, expressed as % (rapid and
useful for comparing two habitats)
cover = the % of ground covered by a species (useful where it is not possible to identify
separate individuals)
abundance = subjective assessment of species present, using the DAFOR scale: D = dominant,
A = abundant, F = frequent, O = occasional, R = rare (same observer must make abundance

judgements, which may be useful as comparisons of two or more habitats, rather than
objective scores)
1m
What is the optimum size of quadrats? This varies
with the habitat and the size of plants found. Look
at the example here. In the 1 m quadrat there are
six species present. How many different species are
counted in the quadrat of sides 10, 20, 30, 40, 50,
60, 70, 80, and 90 cm? The optimum quadrat size
is reached when a further increase in size adds no
or very few further species present.
How many quadrats? When there is no further
increase in the number of species found, sufficient
quadrats have been analysed in that habitat.
1m
70
number of species found in total
60
if more quadrats
50 than about 20 are
used, no additional
40 species are found
(in this habitat)
30
20
10 cm
10 quadrat
0
0 10 20 30 40 50 50 cm
quadrat
number of quadrats analysed
▲ Figure 18.17 Estimating plant populations size using a quadrat
Estimating species distribution by means of a transect

Whereas some communities are relatively uniform over a given area and are suitable for
random analysis (such as the grassland habitat shown in Figure 18.18), others show a trend in
variation in a particular direction. Examples include seashore, pond or lake margin, saltmarsh
or even an area where there is a change from dry soil to wetland. The appropriate technique to
study such a trend of variation is the transect.
Transects are a means of sampling biotic (and abiotic) data at right angles to the impact
of unidirectional physical forces. Although there may only be time to study one transect
in detail (and this may be sufficient as a demonstration of the zonation of communities),
a single transect may not provide an adequate sample or give an indication of differences
from place to place. Transects should therefore preferably be replicated several times.
When transects are carried out across a habitat where the land changes in height and
where level is an important factor (such as a seashore, saltmarsh or pond margin), then
the changes in level along the transect line can be measured and recorded as a profile
transect. The surveying for this requires the use of survey poles and a field level device
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18
18.2 Biodiversity
▲ Figure 18.18 An area of chalk grassland with a rich flora
The community present along a transect can be analysed from a straight line such as a
measuring tape, laid down across an apparently representative part of the habitat. The
positions of every organism present that touches the line are recorded either all the way
along the line or else at regular intervals. The result is a line transect.
A belt transect is a broad transect, usually half a metre wide. To produce it, a tape
measure or rope is laid as for a line transect, but this time the organisms in a series of
quadrats of half-metre width are sampled. When the data from one quadrat has been
collected, the quadrat frame can be flipped over for the next sample. This is repeated
along the length of the transect to obtain a belt of continuous data. Along with data on
the biota, data on abiotic variables can be measured and recorded along the transect.
For example, along a terrestrial transect, the soil pH might be measured.
The results of a belt transect study of a seashore community are shown in Figure 18.19,
overleaf. The seashore (known as the littoral zone) is a part of the extreme margins of
continents and marine islands periodically submerged below sea water, and so affected
by tides. Tides are the periodic rise and fall of the sea level due to the attractions
(gravitational pull) of Moon and Sun. The shore is an area rich in living things, and
almost all are of marine origin.
The higher organisms occur on the shore, the longer the daily exposure to the air the
organisms endure. Exposure brings the threat of desiccation and wider extremes of
temperature than those experienced during submersion. ‘Exposure’ is an abiotic factor
that influences distribution of organisms on the seashore.
Mark, release and recapture (MRR) technique (the Lincoln index)

We have already noted that an important step in determining the biodiversity of an area
is the collection of accurate information on the size of populations present in a habitat.
A total count of all the members of a population is called a census, and would give us
the most accurate data. However, the taking of a census is normally impractical. This
may be because of the size of the habitat, or because of the quick movements of many
animals, or because of species that are only active at dusk or after dark.
The capture, mark, release and recapture (MRR) technique, also known as the Lincoln
index, is a practical method of estimating population size of mobile animals (N), such as
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belt transect study of a rocky shore
18 plants
black lichen (Verrucaria maura)
channelled wrack
(Pelvetia canaliculata)
spiral wrack (Fucus spiralis)
knotted wrack
(Ascophyllum nodosum)
black wrack (Fucus vesiculosus)
serrated wrack (Fucus serratus)
oar weed (Laminaria sp.)
animals
nerite winkle (Littorina neritoides)
rough winkle (Littorina rudis)
edible winkle
(Littorina littorea)
smooth winkle
(Littorina obtusata)
dog whelk
(Nucella lapillus)
barnacle
(Chthamalus montagu)
acorn barnacle
(Semibalanus balanoides)
common limpet (Patella vulgata)
0
high water
50
Key 100
drop in height/cm
rare 150
midshore
occasional 200
250
frequent
300
abundant low water
350
dominant
Question 400
5 From the data 0 2 4 6 8 10 12 14 16 18 20

in Figure 18.19, sampling stations along the transect/m
deduce a plant and
an animal species
that appear to be
profile transect
well adapted to the data obtained by surveying using
degree of exposure survey poles and a levelling device
experienced at
a a high water
location, and
b a low water
location of the
rocky shore.
▲ Figure 18.19 Profile and belt transect analysis of a rocky shore community
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small mammals, woodlice or insects that can be captured and marked with a ring, tag,
or dab of coloured paint or nail varnish.
Of the first sample caught for marking (n1), it is essential to use a method of marking 18
totally resistant to removal by moisture or by deliberate actions of the animals. It must
be a method that does no harm to the captured animals, too. For example, these must
not be more visible and therefore more vulnerable to predation than normal. It is also
essential to trap relatively large samples if the results are to be significant.
The method then requires that marked individuals, on their release, are free to distribute
themselves randomly in the whole population. After randomisation has occurred, a
18.2 Biodiversity
second sample is caught (n2), some of which will be from the first sample, recognised by
their marking (m2). The size of the population is estimated by the formula:
n1 × n2
N=
m2
MRR may be demonstrated on populations of woodlice discovered sheltering under
stones/flower pots, etc. in an area of a garden or woodland. Alternatively, on populations
of night-flying moths via light traps, or on populations of small mammals trapped in
Longworth small mammal traps provided sufficient traps are available, for example.
Prior to experimenting on natural populations, the technique can be learnt and
understood by application to non-living models. These may include beans dispersed
in sawdust, or by using a ‘population’ of dried peas in a hessian bag. Here, samples are
taken by hand, the sampler blindfolded, in effect. These trials enable the accuracy of the
MRR method to be tested because the actual ‘population’ size (beans or dried peas, etc.)
is easily known. It will quickly be evident that the size of samples captured determine
the accuracy of the technique; small samples may give wildly inaccurate estimates. The
steps to the MRR technique are outlined in Figure 18.20, overleaf.
Questions 6 Using MRR, relatively large samples must be caught for significant results. Calculate
the estimated size of the population in Figure 18.20 if the second sample had
included two marked woodlice, not one.
7 As a new habitat was colonised, the size of a population of the common rough
woodlouse Porcellio scaber was investigated by mark, release, recapture, with the
following results:
Day 1/2 15/16 30/31 45/46 60/61 75/76

Captured, marked and released (n1) 7 14 25 19 15 19
Captured in the second sampling (n2) 6 12 24 16 9 14
Marked individuals recaptured (m2) 2 2 3 2 1 2
a Calculate the size of the population at days 2, 16, 31, 46, 61 and 76.
b Plot a graph of estimated population size against time.
c Annotate your graph as fully as you are able.
Analysing relationships between distribution and abundance

of species and abiotic and biotic factors
There are different statistical tests for different kinds of quantitative data. In this case we
are looking for the possibility of an association or correlation between two sets of data.
When one factor is plotted against the other (Figure 18.21, overleaf) then we may find
that:
» both factors increase together, indicating a positive correlation
» one factor increases while the other decreases, indicating a negative correlation
» the scatter diagram appears to have points randomly dispersed, indicating no
correlation.
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18
x
negative
correlation
y
▲ Figure 18.20 Estimating animal populations using ‘mark, release and recapture’
These differences are illustrated in Figure 18.21.

In investigating possible associations there are two issues:
» Is there an association between the two sets of variables?
x
» If so, what is the strength of the association?
no To resolve these issues there are alternative statistical tests according to the type of
correlation
data you have collected – either Spearman’s rank correlation or Pearson’s linear
y
correlation. In Table 18.4 the differences between them are tabulated, and situations in
which they would be chosen listed.
Where your statistical test fits in

When you have decided on an ecological issue to investigate regarding some aspect of
biodiversity in relation to an abiotic factor or another biotic factor, follow these steps:
1 State the null hypothesis (see page 384).
x 2 Conduct your investigation and obtain your data.
positive 3 Present your results in a table and plot a scatter diagram.
correlation 4 Decide on the appropriate statistical test and carry this out (see below).
▲ Figure 18.21 Are the two 5 Draw a conclusion, stating whether you accept or reject the null hypothesis. Add a
variables correlated? statement explaining the significance or implications of your conclusions.
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Spearman’s rank correlation Pearson’s linear correlation
When it is used For ordinal (non-normal) data – values or
observations that can be ranked, counted and
For normal data – values or observations that
can be assigned a number (as a label) but data 18
ordered. cannot be ranked.
Examples How does the population size of grasshoppers How does the height of fathers relate to height
vary in relation to when pesticides were last of their sons or daughters – do taller fathers
applied – are fewer insects found where pesticide have taller children?
application is recent?
How does species diversity relate to latitude –
How do numbers of aquatic stone-fly nymphs does species diversity decrease with distance
18.2 Biodiversity
relate to the hardness of the water – are more from the equator?
nymphs present in hard water?
How does the size of land crabs relate to the
How does the depth of a stream relate to the
density of their burrow – are the burrows of large
proximity of the river bank – does depth of water
crabs more dispersed?
increase with distance from the edge?
▲ Table 18.4 Two tests of association
Carrying out a statistical test

Use a statistical software package or programmed calculator to carry out the test.
An appropriate source, accessed via the web is: Merlin: Statistical Software available
to Biology Students. Merlin is a statistical package produced by Dr Neil Millar.
This software is an add-in for Microsoft Excel. Merlin is available free of charge for
educational and non-profit use. The package may be copied to laboratory and student
computers from: www.stem.org.uk/resources/elibrary/resource/33426/merlin.
Once you have data from laboratory or field investigations, Merlin can be used to carry
out a statistical test. Merlin also includes a basic introduction to statistics for biology
students, and a ‘test chooser’. Data can be displayed in a range of graphs and charts, as
appropriate.
Alternatively if you wish to analyse data by Pearson’s linear correlation, you could use
the following site: www.socscistatistics.com/tests/pearson.
Using Simpson’s index of diversity to calculate biodiversity of a habitat

Early on in the development of a succession, for example at the pioneer stage when new
land is being colonised, the number and diversity of species are low. At this stage the
populations of organisms present are usually dominated by abiotic factors. For example,
if extreme, unfavourable abiotic conditions occur (prolonged, very low temperatures,
perhaps), the number of organisms may be severely reduced.
On the other hand, in a stable climax community many different species are present,
many in quite large numbers. In this situation, adverse abiotic conditions are less
likely to have a dramatic effect on the numbers of organisms present. In fact, in a
well-established community, the dominant plants set the way of life for many other
inhabitants. They provide the nutrients, determine the habitats that exist, and influence
the environmental conditions. These plants are likely to modify and reduce the effects of
extreme abiotic conditions, too.
Thus the diversity of species present in a habitat is also an indicator of the stability
of the community. Species diversity of a community may be measured by applying the
formula, known as the Simpson diversity index:
N(N – 1) where N = the total number of organisms of all species found
diversity D =
∑ n(n – 1) and n = the number of individuals of each species
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Sand deposited by the sea and blown by the wind,
builds into small heaps around pioneer xerophytic
18 plants, such as marram and couch grass, at coasts

where the prevailing wind is onshore. The tufts of
leaves growing through the sand accelerate deposition,
and gradually drifting sands gather a dense cover of
vegetation. Fixed sand dunes are formed.
point frame quadrat in use
Behind the fore dune the fixed dunes can be seen.
The frame is randomly placed a large number of

times, the 10 pins lowered in turn onto vegetation
and the species (or bare ground) recorded.
Study of a sand dune succession from embryo state to fixed dune
Site 1 Site 2 Site 3 Site 4
Stage in succession Embryo dune Fore dune Semi-fixed dune Fixed dune
Number of pins dropped 220 220 220 220
sea couch grass 169 9 0 0
marram grass 1 123 19 0
fescue grass 0 0 126 182
spear-leaved orache 4 0 0 0
prickly saltwort 2 0 0 0
bindweed 1 44 0 0
bird’s foot trefoil 0 0 0 6
biting stonecrop 0 0 0 1
buttercup 0 0 0 1
cat’s ear 0 0 5 2
clover 0 0 0 68
common stork’s bill 0 0 0 11
daisy 0 0 2 8
dandelion (common) 0 0 5 1
eyebright 0 0 0 4
hawkbit 0 0 20 1
ladies bedstraw 0 0 86 35
medick 0 0 0 62
mouse-ear chickweed 0 0 0 2
ragwort 0 0 8 1
restharrow 0 0 25 15
ribwort plantain 0 0 0 37
sand sedge 0 0 32 17
stagshorn plantain 0 0 0 36
tufted moss 0 0 0 119
yellow clover 0 0 0 5
Yorkshire fog 0 0 2 0
wild thyme 0 0 0 82
Total live hits 177 176 330 706
Bare ground hits 48 68 6 0
% bare ground 27 38 3 0
soil moisture (%) 5.0 8.5 16.0 14.3
soil density (g cm–3) 1.6 0.9 0.6 0.5
soil pH 8.0 7.5 7.0 7.0
wind speed (m s–1) 10.0 9.3 2.4 1.3
▲ Figure 18.22 Sand-dune community development – a student field study exercise
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Questions 8 In a vegetable plot left fallow (left unsown, typically for a year), three weed species
appeared. Individual plants were counted: 18
Species n (no. of individuals)
Groundsel (Senecio vulgaris) 45
Shepherd’s Purse (Capsella bursa-pastoris) 40
Dandelion (Taraxacum officinale) 10
Total (N) 95
18.3 Conservation
Calculate the Simpson diversity index for this habitat.
9 Figure 18.22 is a study of the vegetation of a system of developing sand dunes. Note
how both the species diversity and physical parameters change as the dunes age.
Calculate the Simpson diversity indices of the fore dune and semi-fixed dune (using a
spreadsheet). Comment on the results.
18.3 Conservation
Learning outcomes
18.3.1 explain why populations and species can become extinct as a result of:
climate change, competition, hunting by humans, degradation and loss of
habitats
18.3.2 outline reasons for the need to maintain biodiversity
18.3.3 outline the roles of zoos, botanic gardens, conserved areas (including
national parks and marine parks), ‘frozen zoos’ and seed banks, in the
conservation of endangered species
18.3.4 describe methods of assisted reproduction used in the conservation of
endangered mammals, limited to IVF, embryo transfer and surrogacy
18.3.5 explain reasons for controlling invasive alien species
18.3.6 outline the role in conservation of the International Union for the
Conservation of Nature (IUCN) and the Convention on International Trade
in Endangered Species of Wild Fauna and Flora (CITES)
Starting point
★ Maintaining biodiversity is important for many reasons. Actions to maintain
biodiversity must be taken at local, national and global levels. It is important
to conserve ecosystems as well as individual species.
The threats to biodiversity

Evolution, the development of life in geological time, is the process that has transformed
life on Earth from its earliest beginnings to the organisms we know about today,
living and extinct. Biodiversity is a result of 3.5 million years of evolution. Very many
distinctly different organisms have evolved by natural selection and flourished at least
for a while during this long time span. Consequently, today’s biodiversity is only a tiny
proportion of the diverse forms of life that have evolved in total. Most of these organisms
and groups have become extinct.
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The current sharp decline in biodiversity
18 Today, the issue of human influence on biodiversity is an issue of major concern.

Why do you think this is?
In the long history of life on Earth, humans are very recent arrivals. Life originated
about 3500 million years ago, but our own species arose only a little over 100 000 years
ago. Initially, human activities had little impact on the environment. For one thing,
during early human ‘prehistory’, population numbers were low. Homo sapiens were
a rather ‘struggling’ species, living among many very successful ones. At this stage,
survival must have been a very chancy affair.

Look back at Figure 10.2 on page 202.
The first significant increase in the human population occurred with the development
of settled agriculture – a change that began in the fertile crescent in the Middle East
about 10 000 years ago. The current human population explosion began at about the
beginning of the Industrial Revolution, around 200 years ago, and it continues today.
No one is certain when the rate of population growth will slow down, as it surely must.
When we plot world human population against time we see a steeply-rising J-shaped
curve. Our population growth appears to be in an exponential (log) phase of growth.
This is due to high birth rates and lower death rates, leading to rising life expectancy
(people are living very much longer). Today the impact of humans on the environment is
very great indeed – there is virtually no part of the biosphere which has not come under
human influence and been changed to some extent. Many of these changes threaten the
biodiversity in all ecosystems.
Question Only a part of planet Earth, its land, oceans and atmosphere are inhabited. Living things
inhabit a narrow belt, from upper soil to the lower atmosphere, or, if marine, most occur
10 What is the chief
near the ocean surface. This restricted zone is called the biosphere. The distribution
ecosystem in the
patterns of living things within the biosphere show large, stable vegetation zones. These
country where you
live? zones are called ecosystems. Examples include tropical rainforest and grassland. Here
communities typically extend unbroken over thousands of square kilometres.
Why organisms become extinct

The obliteration of the dinosaurs about 65 million years ago has been widely discussed. It
is less well known that at that time almost half the genera of marine non-vertebrates also
became extinct. Moreover, this was only one of several extinction events. The extinctions
at the end of the Permian period, 250 million years ago, eliminated over 80 per cent of the
marine, non-vertebrate genera. The sequence of mass extinctions, obtained by plotting the
rate that genera have died out in a geological period is shown in Figure 18.23.
The significant forces driving extinctions are climate change, competition between
species, whether interspecific or intraspecific, habitat loss, and by human destruction.
Climate change
Coral reefs are one of the ‘theatres of environmental change’ threatened by global warming
(Figure 18.24). Corals are colonies of small animals embedded in a calcium carbonate
shell that they secrete around themselves. They form their underwater structures in warm,
shallow water where sunlight penetrates. Microscopic (photosynthetic) algae live sheltered
and protected in the cells of corals. The relationship is one of mutual advantage (a form of
symbiosis called mutualism), for the coral gets up to 90 per cent of its organic nutrients
from these organisms. Coral reefs are the ‘rainforests of the oceans’ – the most diverse of
ecosystems known. Although they cover less than 0.1 per cent of the surface of the oceans,
these reefs are home to about 25 per cent of all marine species.
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Figure 18.23 The The five big mass extinction events
sequence of mass Ordovician–Silurian Late Devonian Permian Triassic–Jurassic Cretaceous–
extinctions in geological
time
443 million years
ago (mya)
359 mya 248 mya
96% of all species
200 mya Tertiary
65 mya
18
were wiped out All the dinosaurs
were wiped out
Carboniferous
Cretaceous
Ordovician
Cambrian
Devonian
Permian
Jurassic
Silurian
Tertiary
Triassic
18.3 Conservation
rate of extinction of species
500 400 300 200 100 0

geological time/mya
When under environmental stress (for example, high water temperature), the algae are
expelled (causing loss of colour). In addition, much of the carbon dioxide that enters
the atmosphere dissolves in the oceans. With the resulting ocean acidification, coral
cannot absorb the ions they need to build or maintain their calcium carbonate skeletons.
The coral starts to die, and the surrounding marine species, likewise. Mass bleaching
events occurred in the Great Barrier Reef in 1999 and 2002; between 2016 and 2017
it is estimated that half of the coral died because of record extreme heat. Today, coral
reefs are dying all around the world. The effects from thermal stress are likely to be
exacerbated under future climate scenarios.
▲ Figure 18.24 Coral reefs – a crisis situation

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Competition
18 Competition between organisms leading to the extinction of a species is difficult to

establish. We might argue that any species that has become extinct and is known only
as a fossil may be an example, but establishing a link between cause and effect may
be impossible. In the laboratory, we can demonstrate how competition between two
organisms that have the same diet or nutritional requirements and live in the same
habitat (that is, they occupy the same niche) leads to the exclusion of one (Figure 18.25).
This experiment is a demonstration of the competitive exclusion principle.
An experiment carried out by G. C. Gause in 1934 using species of Paramecium, a large protozoan
common in fresh water. It feeds on plankton, the food source used in these experiments.
food vacuoles of
waste disposed of bacteria formed here
gullet (’cytopharynx’)
a feeding current is generated by

cilia in the oral groove
products of digestion
absorbed into cytoplasm
food vacuoles have

digestive enzymes added, direction of movement
first in an acid phase, then
in an alkaline phase
P. aurelia
a smaller,
species cultured separately fast-growing species
200
numbers of Paramecium per
0.5 cm3 of culture solution
150
100
P. caudatum
50 a relatively large,
slow-growing species
0
0 2 4 6 8 10 12 14 16
time in days
species cultured together
200
numbers of Paramecium per
0.5 cm3 of culture solution
150
100 P. caudatum was

competitively excluded
50
0
0 2 4 6 8 10 12 14 16
time in days
▲ Figure 18.25 A demonstration of competitive exclusion
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The history of the evolution of the genus Homo has many examples of species that
became extinct (Figure 18.26). Can we know the actual causes of their extinctions?
Surely we can only guess. 18
Figure 18.26 Some Homo
evolutionary stages in Homo neanderthalensis
hominid evolution earlier, archaic species
sapiens
million
years ago
0
18.3 Conservation
0.5
robust species of
Australopithecus
1
Homo erectus
1.5
2.5 Homo habilis
Australopithecus
3 africanus
3.5
4 Australopithecus
afarensis
4.5
300 500 700 900 1100 1300 1500

cranial capacity/cm3
Hunting by humans
The African elephant (Loxodonta africana) once roamed most of the continent of
Africa. In 1930, it was estimated there were 5–10 million African elephants, but by
1979 their numbers were reduced to 1.3 million. In 1989, when they were added to the
international list of the most endangered species, there were about 600 000 remaining,
less than 1 per cent of their original number. Although still relatively widely distributed
south of the Sahara, populations are now fragmented. Many are restricted to National
Parks and Reserves (Figure 18.27, overleaf). One reason why African governments take
measures to protect elephants at these venues is the importance of the tourist trade to
their economies. Their National Parks bring in much-needed income, and ‘ecotourism’
does not deplete wildlife populations.
Today, elephants are threatened by loss of their habitats, by conflict with humans and
by ivory poaching.
The demand for ivory threatens the largest adults with the biggest tusks. Old
matriarchs (the oldest adult females who provide the ‘social glue’ for the herds) are
particularly vulnerable. Their group existence makes them easier than solitary adult
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males for the poachers to locate. Other people continue to slaughter these magnificent
animals too, for the ‘bush meat’ trade, for example.
18 Encroachment on human settlements is another problem. The hungry elephant that
destroys crops is often hunted down and killed. Moreover, the increasing pressures of
land use, as the wild spaces are deforested or cleared and converted to crop production,
enhances this problem. In East Africa in particular, a high percentage of wildlife lives
outside reserves, and so is not protected. Here, few elephants are now predicted to
survive outside high-security areas. A similar trend is seen in the rest of Africa.
The outcome of these threats to the African elephant is predicted to be extinction in
the wild.
▲ Figure 18.27 An African elephant herd, observed in a National Nature Reserve
A well-documented example of extinction driven by human action is that of the dodo

(Figure 18.28). The dodo was an inhabitant of the island of Mauritius in the Indian Ocean.
It was a bird related to modern pigeons. Over geological time this distinctive organism had
evolved to master a terrestrial habit. In the process it became a large sized bird (it was about
a metre long and had a mass of approximately 20 kg). The dodo nested on the ground and
reared its young there. The diet was one of seeds and fruits that had fallen from the forest
trees. It was one of many forest dwelling birds on the island – one of the 45 species for
which there are early records, of which only 21 species have survived to this day.
The factors that contributed to the extinction of the dodos:
» Mauritius, an island far from any mainland, became a port-of-call for European
explorers in the sixteenth century. Ships’ crews restocked with fresh meat, and
the dodo was one source. The animal was an easy victim; it had previously lacked
significant natural enemies.
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» Later, settlers brought cats, dogs and pigs, and
inadvertently, rats, all alien species that fed on the young
in the dodo’s nest. 18
» Finally, natural habitats of the island were deliberately
destroyed as land was cleared by human settlers for
agriculture production.
Degradation and loss of habitat

Rainforests cover almost 2 per cent of the Earth’s land surface,
18.3 Conservation
but they provide the habitats for almost 50 per cent of all
living species. It has been predicted that if all non-vertebrates
occurring in a single cubic metre of tropical rainforest soil were
collected for identification, there would be present at least one
completely previously unknown species. It is the case that
tropical rainforests contain the greatest diversity of life of any of
the world’s biomes.
Now, tropical rainforests are being rapidly destroyed. Satellite
imaging of the Earth’s surface provides the evidence for this – if
▲ Figure 18.28 The dodo – a reconstruction and where no other reliable sources of information are available.
The world’s three remaining tropical forests
of real size are in South America (around the
number of bird species number of amphibian species
Amazon Basin), in West Africa (around the
Congo Basin) and in the Far East (particularly
but not exclusively on the islands of Indonesia).
The current rate of destruction is estimated to
be about one hectare (100 m × 100 m – a little
larger than a football pitch) every second. This
means that each year an area larger than the
British Isles (31 million hectares) is cleared.
609 131 While extinction is a natural process, this
current rate is on a scale equivalent to that
400 100 at the time of the extinction of the dinosaurs
(an event 65 mya, at the Cretaceous–Tertiary
200 50 boundary).
When the distribution of livings things across
1 1
0 species the Earth’s surface is investigated we find that
most species are not distributed widely at all
▲ Figure 18.29 Most species have small ranges and these are (Figure 18.29). Instead, very many are restricted
concentrated unevenly to a narrow range of the Earth’s surface.
Consequently, when tropical rainforests are
Question destroyed, the only habitats of a huge range of plants is lost, and with them very many
of the vertebrates and non-vertebrates dependent on them, too. This is one major reason
11 Think about and why the fate of the remaining rainforest is such an urgent issue.
research two ways
in which the human The importance of biodiversity
population explosion
The ecological importance of diversity has been discussed above. The need to maintain
represents a threat to
the Earth’s wildlife. biodiversity is also based upon genetic, economic and ecological principles, as well as
upon ethical issues.
Genetic diversity and the evolution of new species

How diversity within a species arises via mutations (page 137) and during meiosis and
fertilisation (pages 348–9) has already been discussed.
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Question In a population, a group of individuals of a species living close together and able to
interbreed, the alleles of the genes located in the reproductive cells of those individuals
18 12 Design a flow chart
that records in
make up a gene pool. A sample of the alleles of the gene pool will contribute to
form the genomes (gene sets of individuals) of the next generation, and so on, from
sequence the sources generation to generation.
of variation that may
arise, starting with The size of an interbreeding population has a direct impact on the genetic diversity of
the genotype of a the individuals. A very small population can be described as an inbreeding group –
parent and leading the individual are closely related. In fact, the smaller the population the more closely
to the distinctive related the offspring will be. The important genetic consequence of inbreeding is that
phenotype of one of it leads to homozygosity – there is progressively less variation in the population as the
its offspring. number of loci at which there are homozygous alleles increases. While the individuals
of that population may initially be well adapted, in the face of environmental changes
they are less able to adapt. We can say that the ‘genetic fitness’ of the population is
compromised.
In the case of small, isolated populations, genetic variability is most critical. For
example, in populations of species that become endangered, it is a question whether
they posses sufficient genetic diversity to be able to adapt to future changes in the
environment. If they do not, their survival is unlikely. This is a practical problem
facing modern zoos attempting captive breeding programmes (page 448). It is also an
issue for other attempts to protect endangered organisms in the wild where population
numbers have been reduced to small, isolated groups in former strongholds.
Genetic diversity as the reservoir of essential genes for agriculture

Our domesticated animals and cultivated plants were derived originally from wild
species. This is the origin of many of the organisms that provide our food, fuel, timber
and pharmaceutical chemicals. Consequently, the wild relatives of domesticated
species are a continuing source of genes for resistance to pests and diseases, and
also to overcome stresses due to drought, rising salinity and extreme temperatures.
For example, some modern crops have had resistance to pathogens added by the
introduction of genes from ‘wild’ relatives. The loss of primitive varieties means the loss
of the genetic variations essential for sustained crop and herd improvement. If genetic
diversity of a species becomes low, the species is at risk, because once genetic variants
are lost they cannot be recovered.
Biodiversity and the origin of new drugs

Many new drugs and other natural products, in some form or another, are extracted
from substances manufactured by plants. The discovery of new, useful substances often
starts with rare, exotic or recently discovered species. The whole range of living things
is functionally a gene pool resource, and when a species becomes extinct its genes are
permanently lost.
Biodiversity and ecotourism

Responsible travel to natural areas which conserves the environment and improves
the welfare of the local people is referred to as ecotourism. The ecotourist seeks to
observe wildlife and habitats that may be unfamiliar to them as well as being fragile
and (hopefully) pristine, for example. Usually, this involves visits to national parks
or special reserves where the diverse, local plants and animals are already conserved
in as natural an environment as possible. The aim is to learn about ecology and
diversity with minimum disruption or destruction, and to empower local and national
communities. This may be by aiding local development funds and resources for their
fight against poverty and disease. Ecotourism aims to support sustainable development
by empowering the local community economically and socially.
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The climatic and scientific importance of biodiversity
As the human population expands and extends its impact on the natural world, the
threat imposed on diverse habitats increases. Yet natural habitats are critically important 18
‘outdoor laboratories’ where we learn about the range of life that has evolved and
how it has evolved. In some habitats, including in tropical rainforests, the majority of
organisms present are as yet unknown. Furthermore, autotrophic organisms everywhere
(algae in the seas, grasses on the plains and prairies and forest and woodland trees) are
all carbon dioxide sinks that help reduce climate change, to varying extents. Change
in global patterns of rainfall result from deforestation, just as changes in wind and sea
18.3 Conservation
current patterns lead to extreme or unusual weather.
The ethical and aesthetic basis for maintaining biodiversity

A diversity of habitats and the wildlife they sustain are more than just exhilarating
venues to visit and be inspired by. They are part of the inheritance of future generations
which should be secured for future people’s enjoyment, too. There is a moral obligation
on humans to pass on to future generations the diversity we have inherited and enjoyed.
Some habitats are also the home of peoples who have avoided ‘development’. These places and
the people who inhabit them have a right to their traditional ways of life. Their livelihoods
and homes are dependent upon the biodiversity they have evolved among and with. Similarly,
many higher mammals, including relatively close relatives of Homo, live exclusively in some of
these habitats. The needs of all primates must be respected, as indeed should the needs of the
plants and animals around them. Damage to marine environments, especially to coral reefs,
has resulted from overfishing and pollution. Marine food chains sustain biodiversity, as well
as the fishing industry and tourism, on which many human communities depend.
Methods of protecting endangered species

Conservation by promotion of nature reserves
size edge Nature reserves are carefully selected land areas
set aside for restricted access and controlled use, to
allow the maintenance of biodiversity locally. This is
effective design
not a new idea; the New Forest in southern Britain
was set aside for hunting by royalty over 900 years
ago. An incidental effect was that it functioned as a
sanctuary for wildlife.
isolation corridors Today, this solution to extinction pressures on

wildlife includes the setting up and maintenance
of areas of special scientific interest as nature
reserves, of national parks (the first national park
was Yellowstone, set up in North America in 1872),
and of the African game parks which have been
more recently established. In total, these sites
represent habitats of many different descriptions,
in many countries around the world. Some of the
ineffective design conservation work they achieve may be carried out
by volunteers.
What biogeographical features of a reserve best promote
conservation?
In a nature reserve the area enclosed is important –
a tiny area may be too small to be effective (Figure
18.30). The actual dimensions of an effective
reserve vary with species size and the lifestyle of the
majority of the threatened species it is designed to
▲ Figure 18.30 Features of effective nature reserves protect.
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Also, there is an edge effect. A compact reserve with minimal perimeter is less effective
than one with an extensive interface with its surroundings. The use of the surrounding
18 area is important, too; if it is managed sympathetically it may indirectly support the
reserve’s wildlife.
Another feature is geographical isolation – reserves situated at a greater distance from
other protected areas are less effective than reserves that are closer together. Also, it has
been found that connecting corridors of land are advantageous. In agricultural areas
these may simply take the form of hedgerows protected from contact with pesticide
treatments that nearby crops receive.
The reserve or park is best managed to the advantage of wildlife by:

» the employment of local people as trained wardens and rangers, who patrol the
area to ensure people comply with local regulations. They note the condition of the
wildlife, record the changing population sizes and protect the wildlife where the
need arises
» the supervision of agricultural and hunting activities, maintaining the emphasis on
traditional practices applied to modest or minimal levels
» the control of permitted industrial activities, typically mining or quarrying, logging,
Question and fishing in marine reserves, and of the associated transport infrastructures needed.
13 What are the
particular challenges For visitors and ecotourists:
in the management » visitor centres are provided and staffed to educate and inform on the local issues of
of a nature reserve conservation
in your locality or
» access is controlled and restricted to specific footpaths, tracks and roads to avoid
country?
critical wildlife habitats.
Continuous monitoring of the reserve so that causes of change are understood, change may be anticipated and measures
taken early enough to adjust conditions without disruption, should this be necessary. For example, coral reefs require
monitoring for the impact of ecotourism.
Maintenance of effective boundaries and the limitation of unhelpful human interference. The enthusiastic involvement
of the local human community communicates the messages of the purposes of conservation (a local ‘education’
programme, in effect) and that everyone has a part to play in conservation.
Also, protection of major migration routes of large herds of herbivores and the big predators that follow them, as in
Africa and North America.
Measures to facilitate the successful completion of lifecycles of any endangered species for which the reserve is
home, together with supportive conditions for vulnerable and rare species.
Restocking and reintroductions of once common species from stocks produced by captive breeding programmes at
zoological and botanical gardens. This makes possible reintroduction of species (usually predators) hunted almost to
extinction in farming areas, including wolves in Europe and in the northern national parks in the USA.
▲ Table 18.5 What active management of nature reserves involves – a summary
Zoological gardens and their captive breeding programmes

Questions Endangered species typically have very low population numbers and are in serious danger
of becoming extinct. For some species whose numbers have declined drastically, captive
14 What is meant by in breeding may be their last hope of survival. Today, many zoos cooperate to manage
vitro and in vivo? individuals of the same species held in different zoos as a single population. A ‘stud book’
15 Outline two ways – a computerised database of genetic and demographic data – has been compiled for many
in which captive of these species. This provides the basis for the recommendation and conduct of crosses
breeding has designed to preserve the gene pool and avoid the problems of inbreeding. Animals may
made an effective be shipped between zoos or the technique of artificial insemination may be used instead.
contribution to Some species can be very hard to breed in captivity, for example, due to the stresses of
the survival of captivity which may disrupt their breeding cycles. With others there has been a high
endangered animal success rate. Captive breeding permits the monitoring of the mother and her fetus during
species. known pregnancies. To bring about pregnancies that are otherwise occurring at low
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frequencies, banks of eggs and sperm can be stored frozen. This allows the use of artificial
insemination and even in-vitro fertilisation techniques (Figure 18.32, overleaf) and the
implantation of embryos in surrogate mothers. 18
A successful outcome is when individuals bred in captivity are released and have
survived in the wild. Examples include red wolves, Andean condors, bald eagles and
golden lion tamarins. However, the release of captive-bred organisms is not always a
success. The destruction of natural habitats may be a problem – for example, natural
food sources may be limited. Animals reared in captivity may not adapt to unfamiliar
surroundings and may easily fall prey to predators. They may experience difficulty in
18.3 Conservation
integrating with remaining wild individuals through failure to communicate. Another
criticism of the process includes the fear that genetic diversity may have so declined
already that a species cannot be regenerated. Also, because the work concentrates on a
few, highly attractive species and the cost is high, funds are diverted from more effective
habitat conservation and it gives a false sense that extinction problems are being solved.
The maintenance of botanic gardens and of seed banks

Questions A seed is the product of sexual reproduction in flowering plants. It contains an
embryonic plant and a food store within a protective structure. Many seeds naturally
16 The survival of enter a period of dormancy on release from the parent plant. The dormancy periods
endangered species are variable, but in many plants, seeds are capable of remaining dormant but viable for
is supported by many years. This latter feature of the seed is exploited in seed banks where conditions
nature reserves and that will extend dormancy are created and maintained.
by captive breeding
programmes at Storing seeds in seed banks is a relatively inexpensive and space-efficient method of
zoos and seed conservation. Here, natural dormant seeds are kept viable for long periods, typically
banks at botanical in conditions of low humidity and low temperature. Figure 18.31 shows one such seed
gardens. By means bank. The steps, following collection and preparation, are:
of a table, contrast » seed drying (to below 7 per cent water)
these approaches, » packaging (in moisture-proof containers)
identifying particular
» storage (at a temperature of −18 °C)
strengths and
» periodic germination tests
possible drawbacks.
» re-storage or replacement.
17 Why do the seeds in
long-term storage in
seed banks have to
be germinated and
new ones stored?
▲ Figure 18.31 Wellcome Trust Millennium Building, Wakehurst Place – home to the
Millennium Seed Bank (an initiative of the Royal Botanic Gardens, Kew, in the UK)
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Samples of individual species of seeds typically take up very little space, so each sample
(consisting of many seeds) can represent a large gene pool that is being preserved.
18 At regular intervals samples are germinated and the plants grown in the facilities of
a botanic garden so that fresh seeds are available to replenish the stores. Seeds are
easily exchanged between botanic gardens internationally, too. The possibility of the
reintroduction of endangered species of plants to their natural habitats is a possible
outcome.
Seeds with very limited longevity are not stored. Typically such species must be maintained
as growing plants in botanic gardens. Cocoa, coconut and rubber are examples.
Use of assisted reproduction in conservation

The introduction of captive breeding programmes was discussed on page 448.
Techniques developed in modern reproductive technology have been adapted for use in
these programmes (Figure 18.32).
Representative endangered species of mammals, held in zoos, may be effectively
conserved by the process of fertilisation of eggs outside the body (in-vitro fertilisation –
IVF). The key step in IVF is the successful removal of sufficient eggs from the ovaries.
To achieve this, normal menstrual activity is temporarily suspended with hormone-
based drugs.
The process is illustrated here in the Giant panda, but has been applied to several other species – in
some cases with marked success.
1 Normal menstrual cycle steps are

blocked, temporarily. (Pituitary
gland activity is suppressed by
injection of a hormone that blocks the
gonadotrophin releasing hormone).
2 Synthetic FSH is injected – ovaries
are stimulated to develop many
3 Sperm collected from
egg cells (superovulation).
males in the same or different
zoos. Sperm stocks can be held
frozen in a viable state for later
use in any participating zoo.
4 Several egg cells are

Giant panda, Ailuropodo removed from the ovaries
positioned with the aid
of ultrasound.
5 Eggs are mixed with sperm

in a shallow dish. Checked
8 Several embryos are transferred
by microscopic examination
into the uterus in the expectation
that some will implant successfully. to ensure fertilisation.
Alternatively, embryos can be

frozen for future use.
6 Zygotes then incubated at body

temperature for 2–3 days.
7 Microscopic examination to confirm that embryos have

reached the 4- to 8-cell stage.
▲ Figure 18.32 The process of in-vitro fertilisation, adapted for animal conservation
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Then the ovaries are induced to produce a large number of eggs simultaneously, at a
time controlled by the team of zoo vets. In this way the correct moment to collect the
eggs can be known accurately. 18
Egg cells are then isolated from surrounding follicle cells and mixed with sperm. Viable
sperms may be held in sperm banks in a frozen state, and therefore can be from male
animals held in zoos elsewhere in the world. In this way, the gene pool of endangered
species is significantly less restricted.
If fertilisation occurs, the fertilised egg cells are incubated so that embryos at the
8-cell stage may be placed in the uterus. If one (or more) imbed there, then a normal
18.3 Conservation
pregnancy may follow. Spare embryos can also be frozen, and they too can be shared
with other zoos.
The young mammals created in this way may be exchanged too, and surrogate mothers
may be used. The steps to IVF as illustrated are routine in principle, but in many
endangered species the success rate has been limited, so far.
Controlling alien and invasive species

Alien species are introduced plants and animals that have been accidentally or
deliberately transferred from habitats where they live, to new environments where the
abiotic conditions are also suitable for them. If the alien takes over local ecosystems in
an aggressive way, detrimental to the food chains of their new habitat, its presence leads
to the decline of native species. The alien is then described as an invasive species.
Grey squirrels
The success of the American grey squirrel (Sciurus carolinensis) in Britain at the expense
of the red squirrel (Figure 18.33) is a good example. The grey squirrel was accidentally
introduced here in the nineteenth century. The red squirrel is now restricted to just two
locations in the UK, having once been widespread over much of the country. The grey
squirrel has spread rapidly, chiefly because:
» It is able to consume a wider range of locally growing nuts (including the very
common woodland oak tree’s acorn that the grey can digest, but which the red
squirrel cannot), together with the hazel nuts and pine cones, the limited diet of the
red squirrel.
» The aggressive and nimble grey squirrel is a fair match for local predators and lacks
some natural predators – alien species are frequently introduced with few if any of
their natural predators.
» The grey squirrels carry the ‘squirrelpox’ virus which kills many red squirrels without
causing any symptoms in the grey squirrel (and the niches of the two species overlap).
Figure 18.33 Red and

grey squirrels
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In woodlands where the grey squirrel has become such an aggressive pest that it
seriously damages young trees, foresters have deployed a chemical method of control.
18 Bait, consisting of maize seeds impregnated with a high dose of oestrogenic chemicals,
has been introduced into woodland during the squirrel’s breeding season. The bait is
protected in dispensers that only the squirrel has easy access to (Figure 18.34). The
outcome is that the fertility of the squirrels is compromised and the local populations
are not maintained – at least for a number of years. This is, in effect, an example of
‘culling’ by contraception.
Rabbits
Another example of an alien species that has become ‘invasive’ is the rabbit (Oryctolagus
sp.), which was deliberately introduced from Europe into Australia in 1859. This
voracious herbivore spread rapidly. No natural predators present were an effective
threat (interspecific competition failed), and rabbits quickly overran large parts of the
continent. Grassland, available to herds of herbivores, principally cows and sheep, was
▲ Figure 18.34 seriously damaged. Agricultural production was plunged into a crisis. This continues,
Contraceptive bait even now, with varying degrees of severity.
deployed for the grey
squirrel population In desperation, and as a biological control measure, myxoma virus that had
been discovered in South American rabbits (a different species from the European
rabbit), was introduced in 1950. Myxoma virus causes a parasitic disease of rabbits,
myxomatosis, but on its ‘home’ continent its effects were mild. The changing effects of
this virus on rabbit mortality (1950–56) are shown in Figure 18.35, as is the resulting
change in virulence of the virus. We may assume that initially, a small number of the
huge population of rabbits had immunity. As their vulnerable relatives were killed off
the immune rabbits prospered from the diminished competition for grass. Rapidly, the
bulk of the population were immune, and any that failed to develop immunity were
quickly taken out.
100 100
rabbit mortality
80
rabbit mortality/%
virus virulence/%
60
90
40
virus
20 virulence
80
0
0 1 2 3 4 5 6
years
▲ Figure 18.35 Changing rabbit mortality and virus virulence, following

introduction of the myxoma virus as a biological control measure
In their original habitat, an ‘alien’ species will have evolved in the company of natural
parasites and predators – and come to exist in balance with other organisms of the
community. In a new habitat, the alien’s natural enemies may be absent, so they grow at
the expense of native species, crowding them out.
Japanese knotweed
A most unfortunate example of this is Japanese knotweed (Fallopia japonica),
deliberately introduced into northern Europe in the early nineteenth century as an
ornamental plant for garden ponds and lakes.
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The advance of Japanese knotweed in the UK is an example of the spread of an invasive
species devoid of the usual limiting factors that keep it under control in its native
Japan (Figure 18.36). Here, knotweed plants grow into dense, submerged thickets that
overshadow and crowd out native water plants, block waterways and public access to
18
stream banks. In Japan, the plant grows in a balanced relationship with other water
plants and causes no significant problems. Meanwhile, in Britain, the chemicals in the
plant’s leaves and roots discourage predation by local leaf browsers or root parasites. In
Japan, predators have evolved that can cope with these defence mechanisms. Farmers,
gardeners and local councils face huge and increasing bills to suppress this rampant
invasive species.
18.3 Conservation
A Up to 1900 B Up to 1920
0 100 km 0 100 km
C Up to 1940 D Up to 1994
0 100 km 0 100 km
▲ Figure 18.36 Distribution of knotweed in the UK, 1900–94
The roles of non-governmental organisations in conservation

International Union for the Conservation of Nature (IUCN)
Currently, the rate of extinctions is exceptionally high. Environmentalists seek the
survival of endangered species by initiating and maintaining local, national and
international action. For example, the International Union for the Conservation of
Nature (IUCN), working with appropriate local organisations, publishes a series of
Regional Red Lists. These assess the risk of extinction to species within countries and
regions. The lists are based upon criteria relevant to all species and all regions of the
world (Figure 18.37, overleaf). They convey the urgency of conservation issues to the
international community and to policy makers. The aim is to stimulate action to combat
loss of endangered species and of the habitats that support them.
You can read more about the work of the IUCN at: www.iucn.org.
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18
▲ Figure 18.37 IUCN Red List data
Convention on International Trade in Endangered

Species of Wild Fauna and Flora (CITES)
The Convention on International Trade in Endangered Species (CITES), was set up
in March 1973 to regulate worldwide commercial trade in wild animal and plant
species. It is one of the largest and oldest conservation agreements in existence. The
aim and goals of CITES are to ensure that international trade does not threaten the
survival of any species. Since its inception, the number of nation states that have
declared their commitment to the convention has reached more than 170. Those
that participate in CITES are obliged to implement decisions in their domestic
legislation programmes.
CITES classifies plants and animals according to three categories, based on how
threatened they are:
1 Species that are in danger of extinction – the commercial trade of these plants and
animals is prohibited outright.
2 Species that are not threatened with extinction but that might suffer a serious decline
in number if trade is not restricted, so their trade is regulated by permit.
3 Species that are protected in at least one country that is a CITES member and that
has petitioned others for help in controlling international trade in that species.
Categories 1 and 2 are effective in global conservation, whereas the impact of Category
3 is in local conservation. In the final analysis, CITES is only effective as long as the
member countries genuinely abide by collective decisions.
You can read more about the work of CITES at: www.cites.org.
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SUMMARY
» The process of classification involves naming eukaryotic organisms, differentiated into tissues.
18
organisms using the binomial system so that each Many are motile organisms. Their nutrition is
has a generic and a specific name. Genera are heterotrophic.
arranged in a hierarchical classification, of which » Biodiversity refers to the vast number of living
the kingdom is the largest and most inclusive things that exist. About 1.7 million different
category. There are five kingdoms. species are known, but a much larger number
» The Prokaryotae (prokaryotes) include the of organisms may exist, undiscovered. The

bacteria, cyanobacteria (photosynthetic forms) need to maintain diversity is based on ecological
and archaebacteria (extremophiles). They are arguments, but includes diversity as the source
unicellular or filamentous prokaryotic organisms of genes for improvement of agricultural crops,
consisting of very small cells, 1–5 μm. Their as a source of new drugs, to resist climate
nutrition is heterotrophic or autotrophic. change, to support ecotourism and for ethical and
» The Protoctista (protoctists) include the algae aesthetic reasons.
(including the multicellular seaweeds), the » A species is a group of individuals of common
protozoa and the slime moulds. They are single- ancestry that closely resemble each other and
celled eukaryotic organisms or, if multicellular, which are normally capable of interbreeding to
not differentiated into tissues. Their nutrition is produce fertile offspring.
heterotrophic or autotrophic. » The exponential expansion of the human
» The Fungi include the moulds, yeasts, population is a relatively recent phenomenon, but
mushrooms and bracket fungi. They are the current size of the human population results
multicellular eukaryotic organisms (except the in huge demands on the Earth’s living space and
unicellular yeasts), not differentiated into tissues resources. Many environments are being degraded
and non-motile. Their nutrition is heterotrophic. and biodiversity is being reduced. Today, species
» The Plantae (the green plants) includes are in danger of extinction due to the loss of their
the mosses, ferns, conifers and flowering natural habitats, changes in the environment or
plants (broad-leaved and the grasses). They due to over-exploitation. These causes are all
are multicellular eukaryotic organisms, attributable to human activity.
differentiated into tissues. The plants are non- » Conservation is the management of resources
motile organisms, but the male gametes of and habitats so as maintain the existing range
mosses and ferns are motile. Their nutrition is of habitats and to attempt to prevent future
autotrophic. reductions in biodiversity. This includes captive
» The Animalia (animals) includes the non- breeding programmes and the establishment and
vertebrates, such as worms and arthropods maintenance of reserves and national parks, where
(which includes the insects), and the vertebrates, there is supervised protection and an opportunity
which include the fish, amphibians, reptiles, for people to learn about biodiversity and its
birds and mammals. They are multicellular conservation.

1 The St Lawrence river in Canada has been identified as an area with very high
biodiversity.
a Explain how the term biodiversity can be considered at different levels. [2]
b The St Lawrence river is rich in species of aquatic mammals, especially
whales.
In spring, thousands of whales swim from the Atlantic ocean up the
St Lawrence river. Thirteen different species of whale have been recorded.
One of these is the blue whale, Balaenoptera musculus.
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Fig. 1.1 is a diagram of a blue whale.
18 dorsal fin
▲ Fig. 1.1
Photographs of blue whales are analysed by computer so that individual whales

can be identified and population abundance can be estimated. Each blue whale
is different in colour and in the shape of dorsal fin. Different whales also have
different patterns of scarring.
i State the two sources of phenotypic variation in the blue whale population.
[1]
ii Suggest one reason why it is difficult to measure the actual population size
of the blue whale. [1]
c The St Lawrence river runs through very busy industrial areas. It has many
ports for cargo ships, a good fishing trade and many whale-watching boat trips
for tourists.
Decades of whale hunting has caused a large decrease in whale population
sizes. Since whale hunting was banned, whale populations have not recovered.
Seven of the thirteen whale species in the St Lawrence river have been rated as
endangered species.
Suggest two reasons why the populations of whales have not recovered since
the ban on whale hunting. [2]
d Fat samples from under the skin of individual whales of several different
species were taken. These were analysed and the concentrations of the toxins
DDT and PCBs were measured.
Suggest why whales were found to have accumulated very high concentrations
of DDT and PCBs in their fatty tissues. [2]
e Algal blooms sometimes occur in the area of the Atlantic Ocean near the
St Lawrence river. These result from rapid population growth of unicellular
algae such as Alexandrium tamarense.
i A. tamarense produces saxitoxin, a neurotoxin that causes muscle paralysis
by acting on voltage-gated sodium ion channels in neurones. Saxitoxin can
kill whales.
Suggest how saxitoxin results in the death of a whale. [2]
ii Algae, such as A. tamarense, used to belong to the kingdom Plantae but are
now classified in the kingdom Protoctista.
State one reason why A. tamarense is classified in the kingdom Protoctista
and not in the kingdom Plantae. [1]
[Total: 11]
2 The African elephant once roamed most of the continent of Africa. The table below
gives data on more recent estimates of the population size of this giant herbivore.
Date of estimate Population size

1930s 5–10 million
By 1979 1.3 million
By 1989 600 000 (< 1% of original numbers)
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a O utline the diverse range of factors that are most likely to have directly
contributed to this decline. [12]
b If herds of the African elephant continue to decline sharply, explain what 18
impact this is likely to have on heterozygosity in these animals and the
impact this change is likely to have. [8]
[Total: 20]
3 The Sulawesi macaque, Macaca nigra, is found on the large island of Sulawesi in
Indonesia. The Sulawesi macaque is also found on other smaller islands close to
Sulawesi, such as the island of Bacan.
Fig. 3.1 shows a Sulawesi macaque.

▲ Fig. 3.1
a The International Union for Conservation of Nature (IUCN) is the world’s largest
global environmental organisation. The IUCN Red List of Threatened Species™
evaluates the conservation status of plant and animal species. The Sulawesi
macaque is categorised as critically endangered on the IUCN Red List.
Table 3.1 shows the numbers of humans and the numbers of Sulawesi
macaques on Sulawesi and Bacan.
Number Number of
Area/ of Number of Number of macaques per
Island km2 humans humans per km2 macaques km2
Sulawesi 174 600 17 360 000 99.42 5200
Bacan 1900 60 741 31.97 90 000 47.37
▲ Table 3.1
i Calculate the number of macaques per km2 for Sulawesi. [1]

ii Comment on the data shown in Table 3.1 and suggest reasons for the
pattern shown. [3]
b Suggest ways of protecting the Sulawesi macaque. [4]
[Total: 8]
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A LEVEL
The discovery in the early Learning outcomes

1950s of the structure of
DNA by Watson and Crick, By the end of this topic, you should be able to:
supported by the work 19.1.1 define the term recombinant DNA
of Franklin, Wilkins and 19.1.2 explain that genetic engineering is the deliberate manipulation of genetic
Chargaff, and discoveries material to modify specific characteristics of an organism and that this may
since, have led to many involve transferring a gene into an organism so that the gene is expressed
applications of genetic
19.1.3 explain that genes to be transferred into an organism may be: extracted
technology in areas of
medicine, agriculture and
from the DNA of a donor organism, synthesised from the mRNA of a donor
forensic science. This topic organism, synthesised chemically from nucleotides
relies heavily on prior 19.1.4 explain the roles of restriction endonucleases, DNA ligase, plasmids, DNA
knowledge of DNA and polymerase and reverse transcriptase in the transfer of a gene into an
RNA structure and protein organism
synthesis from the topic on 19.1.5 explain why a promoter may have to be transferred into an organism as
Nucleic acids and protein well as the desired gene
synthesis (Topic 6).
19.1.6 explain how gene expression may be confirmed by the use of marker
Candidates will benefit genes coding for fluorescent products
from carrying out practical 19.1.7 explain that gene editing is a form of genetic engineering involving the
work using electrophoresis,
insertion, deletion or replacement of DNA at specific sites in the genome
either with DNA or specially
prepared dyes used to 19.1.8 describe and explain the steps involved in the polymerase chain reaction
represent DNA. (PCR) to clone and amplify DNA, including the role of Taq polymerase
19.1.9 describe and explain how gel electrophoresis is used to separate DNA
fragments of different lengths
19.1.10 outline how microarrays are used in the analysis of genomes and in
detecting mRNA in studies of gene expression
19.1.11 outline the benefits of using databases that provide information about
nucleotide sequences of genes and genomes, and amino acid sequences of
proteins and protein structures
Starting points
★ Genetic 19.1 Principles of genetic technology
engineering
involves the Introducing genetic engineering
manipulation of Genetic engineering is the technique of deliberately manipulating the genetic constitution
naturally occurring of an organism, brought about by means other than conventional breeding and which
processes and usually would not occur in nature, to modify its characteristics. It involves the transfer
enzymes. of a gene or genes and other sequences from one species to another – often an unrelated
★ Genome species – so that the host organism is able to express a new gene product. The outcome
sequencing gives is new varieties of organisms, often (but not exclusively) of microorganisms. These
information about are described as genetically modified (GM) or transgenic organisms containing
the location of recombinant DNA. This type of DNA is formed by laboratory techniques, bringing
genes and provides together genetic material from different sources. Transgenic organisms produce, in their
evidence for the cells, proteins that were not previously part of their species proteome. The proteome is the
evolutionary complete set of proteins that a cell or organism can make. These additional proteins, many
links between of them enzymes, have been engineered with the intention of bringing about significant
organisms. change in the host organism, usually with a specific purpose in mind.
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The techniques of the genetic engineer offer numerous practical benefits in
biotechnology, medicine and agriculture, and also to science and the study of how genes
operate in the control of the cells of organisms. At the same time, outcomes of genetic
engineering may generate environmental and ethical issues of concern to society. We
19
will return to this issue later.
Other applications
Today, in addition to the creation of GM organisms, gene technologies are applied to:
Question » DNA sequencing – the creation of genomic libraries of the precise sequence of
19.1 Principles of genetic technology

nucleotides in samples of DNA of individual organisms. The nucleotide sequence in
1 You have studied how the whole human genome was the product of the Human Genome Project. Today,
the virus called HIV other genomes have been completely sequenced, including those of some viruses,
infects a human cell bacteria, fungi and many other eukaryotes.
(page 212). What is » Genetic fingerprinting – in which DNA is analysed in order to identify the individual
the role of reverse from which the DNA was taken to establish identity and the genetic relatedness of
transcriptase in this
individuals. It is now commonly used in forensic science (for example to identify
process?
someone from a sample of blood or other body fluid). It is also used to determine whether
individuals of endangered species in captivity have been bred or captured in the wild.
The gene technologist’s tool kit
It is the discovery and isolation of four naturally occurring enzymes that make possible
the manipulation of individual genes. We have already met these enzymes in other
contexts, but it is significant that, in this context, some of the enzymes used are now
obtained from bacteria we call extremophiles (page 417). In these organisms, cells (and
therefore their enzymes) are adapted to function at optimum rates under some extreme
conditions, including, for example, very high or low temperatures. We shall discuss how
these enzymes work shortly. They are introduced in Table 19.1.
These enzymes are extracted mainly from microorganisms or viruses and are used to manipulate nucleic acids in very
precise ways
Enzyme Natural source Application in genetic engineering
Restriction Cytoplasm of bacteria (combats viral infection Breaks DNA molecules into shorter lengths, at specific
endonucleases by breaking up viral DNA) nucleotide sequences
DNA ligase With nucleic acid in the nucleus of all Joins together DNA molecules during replication of DNA
organisms
DNA With nucleic acid in the nucleus of all Synthesises nucleic acid strands, guided by a template
polymerase organisms strand of nucleic acid
Reverse In retroviruses only Synthesises a DNA strand (cDNA) complementary to an
transcriptase existing RNA strand
▲ Table 19.1 The genetic technologist’s toolkit of enzymes
Gene technology – an early break through
One of the earliest successful applications of these techniques was when the human
genes for insulin production were transferred to a strain of the bacterium Escherichia
coli (Figure 19.1). Insulin consists of two short polypeptides linked together by sulfide
bonds. Once the hormone is assembled from its component polypeptides, it enables
body cells to regulate blood sugar levels (page 296). Regular supplies of insulin are
required to treat insulin-dependent diabetes. Cultures of E. coli have been ‘engineered’
to manufacture and secrete human insulin when cultured in a bulk fermenter with
appropriate nutrients. The insulin is extracted and made available for clinical use.
1 getting a copy of 2 gene into vector 3 vector into 4 detecting 5 switching on

the gene to be for transport to bacterium transformed gene action
engineered new organism bacteria
▲ Figure 19.1 The steps in the genetic engineering of E. coli for insulin production
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Question The steps in the genetic engineering of E. coli for insulin
production
19 2 Outline
Step 1: Obtaining a copy of the human insulin gene by isolating mRNA
a why we describe
DNA as double One way to obtain a copy of the gene for insulin involves starting with messenger RNA, rather
stranded than searching for the gene itself among the chromosomes. The human pancreas contains
b where DNA patches of cells (the islets of Langerhans, Figure 14.4, page 295) where insulin is produced.
polymerase occurs Here the relevant gene in the nuclei of the cells is transcribed to produce messenger RNA.
and its role in the This passes out of the nucleus to the ribosomes in the cytoplasm. Here the base sequence of
cell.
the RNA is translated into the linear sequence of amino acids of the insulin protein.
There is a particular advantage in making a copy of a gene from the messenger RNA it
codes for. This is explained later in this topic. First, however, the process. This involves:
» messenger RNA for insulin being isolated from a sample of tissue from a human pancreas
» the use of the enzyme reverse transcriptase (obtained from a retrovirus other than
HIV), alongside the isolated messenger RNA to form a single strand of DNA
» the conversion of this DNA into double-stranded DNA using DNA polymerase
(Figure 19.2). In this way the gene is manufactured. This form of an isolated gene is
known as complementary DNA (cDNA).
Figure 19.2 The steps:

Using reverse
transcriptase to 1
build the gene for human pancreas – here insulin is synthesised in β cells of
mRNA extracted islets of Langerhans – so mRNA for insulin production
human insulin from tissue from may be extracted from this tissue
the pancreas
purified mRNA
coding for insulin
A U G G A A C A C U G G C A C C G U U G C U GU
2
reverse transcriptase enzyme added – this synthesises a
synthesis of cDNA mRNA strand
complementary strand of DNA (using a pool of nucleotides)
by base pairing with the sequence of bases of the mRNA is then
discarded
mRNA being used as a template

for DNA synthesis
3
A U G G A A C A C U G G C A C C G U U G C U GU
mRNA strand
discarded cDNA strand
T G T G A C C G T G G C A A C G A CA
– DNA complementary to
base sequence of mRNA
4 cDNA being used as a template

for DNA synthesis
DNA polymerase
synthesises
complementary
DNA strand DNA polymerase
enzyme added – T A C C T T G T G A C C G T G G C A A C G A CA
this synthesises a second
DNA strand, complementary T G G C A C C G T T G C T G T
forming to the base sequence of
cDNA
copy of human
gene for insulin
the two DNA strands T A C C T T G T G A C C G T G G C A A C G A CA
are the gene for insulin
A T G G A A C A C T G G C A C C G T T G C T G T
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Once the gene is isolated, the double-stranded DNA undergoes amplification; many
copies are made. There are various situations in which a genetic engineer is able to
produce or recover only a very small amount of DNA (such as at a crime scene). It is now
possible to submit such minute DNA samples to a process known as the polymerase
19
chain reaction (PCR). In the polymerase chain reaction, DNA is replicated in an
entirely automated process, in vitro, to produce a large number of copies (Figure 19.3). A
single molecule is sufficient as the starting material, should this be all that is available.
The products are always exact copies. The heat-resistant polymerase enzyme used in
this process is known as Taq polymerase after the thermophilic bacterium, Thermus
aquaticus, found in hot springs and hydrothermal vents, from which it was originally

isolated. This protein is able to remain an effective catalyst at a temperature of 97.5°C for
the length of time required in the PCR.
The polymerase chain reaction

The steps to the polymerase chain reaction are of special interest because they show us
how important to genetic engineering was the discovery of the extremophiles with their
uniquely adapted enzymes.
The polymerase chain reaction involves a series of steps, each taking a matter of minutes.
The process involves a heating and cooling cycle and is automated.
Each time it is repeated in the presence of excess nucleotides, the number of copies of the
original DNA strand is doubled.
1 Double-stranded DNA with

known end sequences
5’ 3’
3’ 5’
2 Separate chains by
heating to 95 °C
5’ 3’
3’ 5’
3 Make primer that matches the

end sequences of the DNA
6 Repeat process
fragment to be copied.
using the two new
Cool to 40 °C to allow the
double strands
primer to stick to each strand
5’ 3’
3’ 5’
5’ 3’
3’ 5’
5’ 3’
3’ 5’
4 Add heat-tolerant
Taq polymerase and
nucleotides, and 5 Nucleotides added to primers using
heat to 72 °C single strand as template
Note: ‘Primers’ are short sequences of single-stranded DNA made synthetically with base
sequences complementary to one end (the 3‘ end) of DNA.
Remember: DNA polymerase synthesises a DNA strand in the 3’ to 5’ direction.
Figure 19.3 The polymerase chain reaction
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Question Step 2: Inserting the DNA into a plasmid vector
19
In genetic engineering it is the plasmids of bacteria that are commonly used as the
3 a What is meant by vector for the transference of amplified genes. Many bacterial cells have plasmids
sticky ends?
in addition to their chromosome. These are small, circular, double-stranded DNA
b How does a sticky molecules that are passed on to daughter cells when the bacterium divides. They were
end attach to a seen in Figure 1.24 (page 24) and are shown in Figure 19.5. Plasmids are isolated from
complementary the cytoplasm of a sample of the strain of bacteria being used for the amplification
sticky end? process.
The DNA of the plasmid is cut open using a restriction endonuclease. The restriction
endonuclease chosen cuts the DNA at a specific sequence of bases, known as the
restriction site. The restriction endonuclease selected leaves exposed specific DNA
sequences, referred to as sticky ends. These are short lengths of unpaired bases and are
formed at each cut end (Figure 19.4).
DNA strand, e.g. human gene

isolated plasmid
cut cut Restriction
↓ ↓ cut
G AA T T C GAA T T C endonuclease
↓ recognises particular
GAA T TC
base sequences in
C T T AAG
↓ C T T AAG ↓ DNA and cuts the
C T T AAG double helix at these
cut cut ↓
plasmid cut by cut particular points,
DNA strand cut by restriction endonuclease leaving sticky ends.
restriction endonuclease that recognises the
that recognises the sequence GAATTC
sequence GAATTC
‘sticky
‘sticky end’ end’
AA T T AAT T
T T
T T AA AA
‘sticky end’ ‘sticky
end’
base pairing occurs at
Splicing means the complementary sticky ends
gene has been inserted
into a gap formed in
the plasmid to form a
complete ring of DNA ligase catalyses
with an extra gene. ligase catalyses
formation of a formation of a
C–O bond here C–O bond here
AA T
TT
AA T Ligase joins the sugar-
TT phosphate backbones
AA AA
T T ligase catalyses of the paired sticky ends.
ligase catalyses formation of a
formation of a C–O bond here
C–O bond here
▲ Figure 19.4 Gene splicing – the role of the restriction endonuclease and ligase
Sticky ends with the same sequence as those on the plasmid are also created on the
isolated insulin gene. This is done by adding short lengths of DNA that are then
‘trimmed’ with the same restriction endonuclease. In this way complementary ‘sticky
ends’ now exist at the free ends of the cut plasmids and the cDNA of the insulin gene,
making it possible for them to be ‘spliced’ together into one continuous ring of DNA.
The enzyme ligase catalyses the formation of a new C–O bond between ribose and
phosphate of the DNA backbones being joined together. Energy from ATP is needed to
bring the reaction about. The steps are summarised in Figure 19.5.
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EXTENSION
19
A note on restriction endonucleases
Restriction endonucleases occur naturally in bacteria. They are believed to have
evolved as a defence mechanism against invading viruses because inside the
bacterial cell they selectively cut up foreign DNA. Many different restriction
endonucleases have been identified as useful by genetic engineers. They are named
after the bacterium from which they are isolated (genus, species and strain).

Name Source organism Recognition sequence
EcoRI Escherichia coli GAATTC
BamHI Bacillus amyloliquefaciens GGATCC
HindIII Haemophilus influenzae AAGCTT
▲ Table 19.2 Some commonly employed restriction endonucleases
plasmid in circular cell wall

the cytoplasm chromosome
bacterium
TEM of cytoplasm of a bacterium, showing

numerous plasmids (×55 000)
break up of cells, and
separation of contents by
centrifugation
TC G
CT
AATTC T AG
AA AG
G
GAA
TTC
CTTA
TA
CTTAA G
isolated
plasmid
a restriction to the cut plasmid open plasmids and recombinant plasmid

endonuclease gene fragments have the enzyme ligase
cutting DNA, e.g. at complementary stick joins
the base sequence ends (the exposed the paired
GAATTC, is now used bases pair up) sticky ends
cDNA of ligase
insulin gene
with sticky ends
AATTC G NNG AA T TC NN NN
G CTTAA
N N C T T A AG N N N N
▲ Figure 19.5 Using a plasmid as the vector for the insulin gene
Step 3: Inserting the plasmid vector into the host bacterium

In the next step, recombinant plasmids have to be returned to bacterial cells. This is a
challenge, since the cell wall is a barrier to entry. The ways this may be done are shown
in Figure 19.6, overleaf. Once this has been brought about, the bacteria are described as
transformed.
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C G
19 AG C
TT
AA
AA bacterial cell
TTC
CTTA
TTA
entry to intact bacterial cells by
AC
temporary creation of
‘zapping’ – treatment with tiny pores in
brief electric shock walls of host bacteria,
recombinant allowing entry of
or recombinant plasmids
plasmids
G treatment with ice-cold

C
AG C
TT
CaCl2 solution, followed by

AA A
AA
CTTA
TTA
brief incubation at 40 °C
TTC
C
transformed
bacteria
▲ Figure 19.6 The return of recombinant plasmids to the bacterium
Step 4: Identifying transformed bacteria prior to cloning

Unfortunately, only a limited number of the cells of a culture of bacteria, treated as
shown in Figure 19.6, will have successfully taken up recombinant plasmids and thus
be able to synthesise insulin. The proportion of transformed bacteria may be as low as
1 per cent. It is only these bacteria that should be cloned and then cultured in a
fermenter if a significant amount of product (insulin) is to be produced. One way
they have been selected is by the use of plasmids with antibiotic resistance genes
(R-plasmids). The process is summarised in Figure 19.7.
Note that while the antibiotic resistance genes of R-plasmids were the first used markers,
because of specific long-term safety issues that their use raises, other markers have been
developed. We return to this issue later.
Step 5: Switching on gene action – why promoters are needed
The next stage is for the transformed bacteria to be cloned and then cultured in a
fermenter. At this point the transferred gene needs to be ‘switched on’ so that the
required protein – in this case, insulin – is produced in significant quantities. This
product may then be extracted from the medium and purified.
In the living cell, some genes are expressed throughout the life of the cells, normally at
quite low concentrations. We can assume in these cases that the proteins coded for are
required constantly.
Other genes have to be activated, or switched on, first. One very efficient switch
mechanism is the lac promoter, a promoter found in prokaryotic cells activated by the
presence of lactose in the growth medium. A human gene such as the insulin gene,
which is from a eukaryotic cell, has to be transferred into an expression vector, such
as a plasmid so that a lac promoter occurs alongside it. The result is that, when lactose
is present in the medium, recombinant bacteria containing this expression vector will
be activated to produce large quantities of the desired polypeptides, insulin in this case,
which can then be extracted.
Quaternary insulin production
We have already noted that although insulin is a relatively small protein, it has quite a
complex quaternary structure (page 50). Insulin actually consists of two polypeptide
chains, A and B, joined together by covalent disulfide bonds (–CH2–S–S–CH2–). Two
separate genes code for the two polypeptides that make up insulin.
As a consequence, separate plasmids have to be engineered for the two chains of insulin, A
and B. Genetically engineered E coli containing both types of plasmid are then selected.
A ‘start’ codon (ATG, also the code for methionine – see Figure 6.11, page 131) has to
be inserted appropriately to the cDNA for both chain A and B. To stop the transcription
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process at the correct place, the ‘stop’ triplet codes (TAA followed by TAG) are added
at the end of the cDNA, too. In this adjusted condition, both genes were added into
plasmids with lac promoters. 19
Finally, when the two polypeptide chains are separated from the bacteria they are
treated first with cyanogen bromide to cut them free from the longer polypeptide chain
at the methionine amino acid. Then they are further treated to promote disulfide bond
formation and development of a quaternary structure.
special plasmid with genes for insulin gene

antibiotic resistance – one gene giving fragments

resistance to tetracycline, and
one giving resistance to ampicillin
insulin
gene added
gene for
tetracycline
resistance
restriction endonuclease
used cuts open the plasmid,
cutting within the
tetracycline gene recombinant plasmid –
tetracycline gene is plasmids introduced
now inactivated to bacteria
+ many unchanged
gene for plasmids
ampicillin
resistance
samples of the culture are plated out on to a

non-selective medium on which all bacteria
will grow. From this master plate replica plates
are made using a sterile replica plating pad
(shown below)
then a sample of the culture on the

master plate is transferred to a plate
plate B with
with the medium and antibiotic present disc covered
tetracycline
with sterile
cloth
plate A with
ampicillin
replica plating – a sterile pad

is pressed on to plate A and
then on to plate B – so the
bacterial colonies grow in only bacteria with a tetracycline
exactly the same pattern resistance plasmid can grow
only bacteria with R-plasmids can here (second selection step)
grow here (first selection step)
the bacteria of this colony

failed to grow on plate B,
and therefore contain
recombinant plasmids
these bacteria are now cultured in the

laboratory to confirm they produce
insulin (final selection step), prior to
culturing in an industrial fermenter
all other bacteria are discarded
(commercial insulin manufacture)
▲ Figure 19.7 The use of R-plasmids for selecting genetically modified bacteria
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Question A new development in insulin production
19 4 Distinguish between
All this was part of the original process of producing human insulin from E. coli. The
complications of producing human insulin from transformed bacteria have now been
a genotype and overcome by genetically engineering yeast cells for insulin production, rather than
genome E. coli. Remember, yeast is a eukaryotic cell with a range of organelles, but it also contains
b restriction plasmids. In eukaryotic cells, proteins for secretion from the cell are manufactured by
endonuclease and ribosomes of the rough endoplasmic reticulum and transferred to the Golgi apparatus
ligase (Figure 1.15, page 17). Here, insulin is converted into its normal quaternary structure
c a bacterial prior to discharge from the transformed yeast cells. However, since yeast is a eukaryote,
chromosome and a the lac operon must be replaced by genes for promoters and other control sequences, in
plasmid. addition to the insulin genes in the ‘engineered’ plasmids. Remind yourself of the control of
gene expression in eukaryotes, on page 374.
Genetic modification of eukaryotes

Manipulating genes in eukaryotes is a more difficult process than it is in prokaryotes.
The reasons for this include:
» plasmids, the most useful vehicle for moving genes, do not occur in eukaryotes
(except in yeasts) and, if introduced, may not survive and be replicated there
» eukaryotes are diploid organisms so each gene occurs twice in the nucleus of a cell,
once on each of the homologous chromosomes, and may occur in different forms
(alleles). Prokaryotes have a single, circular ‘chromosome’, so only one gene has to be
engineered into their chromosome
Question » the transcription of eukaryotic DNA to messenger RNA is more complex than in
prokaryotes; it involves the removal of short lengths of ‘non-informative’ DNA
5 Why are the genes of
sequences, called ‘introns’
prokaryotes generally
» the mechanism for triggering gene expression in eukaryotes is more complex than in
easier to modify than
prokaryotes. Genes for the promoter and other control sequences have to be
those of eukaryotes?
transferred, as well as the desired gene.
Despite these difficulties, several varieties of transgenic plants and animals have been
produced.
Alternative markers for genetic engineering

A marker is a gene that is deliberately transferred along with the required gene during
the process of genetic engineering. It is easily recognised and used to identify those cells
to which the gene has been successfully transferred. In the production of insulin in
E. coli the original markers were antibiotic resistance genes (Figure 19.7).
Now alternative markers are preferred. This is because of the potential danger of the
antibiotic resistance genes being accidentally transferred to other bacteria, including
eventually, pathogenic strains of E. coli or even pathogens causing other diseases.
While this has not been reported, the possibility must exist. The outcome would be an
‘engineered’ disease-causing microorganism that was resistant to one or more antibiotic.
Genes for fluorescent (or easily stained) substances are now used as markers (Figure 19.8)
instead of antibiotic resistant genes, alongside the cDNA of the desired gene. These genes
are then linked to a special promoter. The marker gene is expressed only when the desired
gene has been successfully inserted into the genome of the host. Organisms that have been
transformed in this way will glow under UV light (or can be identified by staining).
Other methods of isolating genes for gene technology

Converting messenger RNA that codes for the insulin genes into cDNA, as described
above, has the advantage of yielding the gene without the short lengths of ‘nonsense’ DNA
(known as introns). After transcription of the coding strand in the nucleus this editing is
a natural and essential stage. It is not easily for a genetic engineer to carry this out in vitro.
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The crystal jellyfish (Aequorea victoria) occurs in the Fluorescence is due to the presence of
plankton off the west coast of North America. It shows a green fluorescent protein (GFP). This
bright green fluorescence when exposed to light in the blue
to ultraviolet range.
protein and the gene that codes for it have
been extracted. 19

The tertiary structure of GFP protein
The GFP gene is now used as a marker The GFP gene has been introduced and maintained in
gene in genetic engineering. For the genome, and then expressed in species of bacteria,
example, it may be inserted into plasmids yeast, fish, plants, insects and mammals. For example,
alongside a cloned gene and its promoter. these GM mice glow green under blue light because the GFP
When these plasmids are returned to gene has been introduced into their DNA.
bacteria and the promoter is activated, the
transformed bacteria will be detected by
exposure to blue light.
plasmid
cloned gene
GFP gene
promoter
The tertiary structure of GFP protein
▲ Figure 19.8 The use of fluorescent markers
There are alternative methods. For example, it is possible to synthesise a copy of the
gene in a laboratory if the linear sequence of amino acids of the polypeptide or protein
is known. The data in the DNA genetic dictionary (Figure 6.11, page 131) gives the
sequence of nucleotides from which to construct a copy of the gene.
As a result of the Human Genome Project (HGP), the location of each human gene
and the base sequence within its DNA structure are known. Now, where a single-
stranded DNA probe, complementary to a particular gene can be produced and
made radioactive or fluorescent in ultraviolet light, original genes can be located and
isolated. To do so, the DNA has first to be cut into fragments. Fragments are then
denatured into single strands by heating, separated by means of electrophoresis
(Figure 19.9, page 469), and then treated with the probe. The fragments of DNA
containing the gene are located.
Both of these methods are currently applied to isolate genes required for other gene
technology projects.
Gene editing
Gene editing is a type of DNA engineering that allows genetic material to be added,
removed or altered at specific locations in the genome. Nearly all diseases have a
genetic component. Some diseases are caused by mutations that are inherited, such as
haemophilia or cystic fibrosis. Other diseases are caused by mutations acquired in a
gene or group of genes during a person’s life. Most mutations occur randomly; others
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are due to exposure to mutagens or some environmental factors such as radiation.
Gene editing offers the possibility of treating diseases by cutting out or replacing faulty
19 (mutated) genes.
Most of the current work is being carried out in mice and zebrafish because the majority
of their genes are the same as those of humans. By changing one or several genes in an
animal, scientists can observe how these changes affect the animal’s health and predict
how similar changes might affect human health.
The first genome editing technologies (zinc-finger nucleases (ZFN) and transcription
activator-like effector nucleases (TALENs)) were developed in the late 1900s and early
2000s. These are difficult to carry out, time-consuming, extremely expensive and
require expertise in molecular biology to produce modified endonuclease enzymes. The
use of these techniques has resulted in modified cells that can be used in gene therapy
and the improvement of crop plant products. They are still used in research labs as they
are more specific than CRISPR (see below). The first clinical use in humans (in 2015)
used a TALEN-based gene editing system to modify T-cells to treat leukaemia.
A more recent genome-editing tool called CRISPR (clustered regularly interspaced short
palindromic repeats) was developed in 2009. CRISPR is much simpler, faster, cheaper,
and does not require as much expertise in molecular biology.
With CRISPR, researchers create a short RNA template that matches a target DNA
sequence in the genome. This is introduced into a eukaryotic cell and binds to the target
DNA. Creating synthetic RNA sequences is much easier than engineering enzymes as is
required for ZFNs and TALENs. A plasmid containing Cas9 genes is then inserted into
the cell and codes for an enzyme Cas9. The RNA portion of the CRISPR, called a guide
RNA, directs the Cas9 enzyme to the targeted DNA sequence. (Cas9 is a restriction
endonuclease enzyme present in certain bacteria that protects the bacteria against
infection by viruses by cutting viral DNA.) Cas9 cuts the genome at this location to
make the edit. CRISPR can make deletions in the genome and or be engineered to insert
new DNA sequences. As Cas9 is guided by the RNA attached to the target DNA it can
cut at almost any point in a DNA molecule.
Even though CRISPR is more efficient and cheaper to use, it is still in the experimental stage.
Electrophoresis
Electrophoresis is a process used to separate molecules such as proteins and
fragments of nucleic acids. It is widely applied in many studies of DNA. For example,
it is central to the investigation of the sequence of bases in particular lengths of
DNA, known as DNA sequencing. It is also used in the identification of individual
organisms and species known as genetic fingerprinting. We will review these
applications shortly.
The principle and practice of electrophoresis

In electrophoresis, proteins or nucleic acid fragments (either DNA or RNA) are
separated on the basis of their net charge and mass. Separation is achieved by
differential migration of these molecules through a supporting medium – typically either
agarose gel (a very pure form of agar) or polyacrylamide gel (PAG). In these substances
the tiny pores present act as a molecular sieve. Through these gels, small particles can
move quite quickly, whereas larger molecules move much more slowly.
Molecules separated by electrophoresis also carry an electrical charge. In the case
of DNA, it is the phosphate groups in DNA fragments that give them a net negative
charge. Consequently when these molecules are placed in an electric field they migrate
towards the positive pole (anode). The distance moved in a given time will depend on
the mass of the molecule or fragment – the smaller fragments moving further in a given
time than the larger fragments. So, in electrophoresis, separation occurs by the size
and by the charge carried. This is the double principle of electrophoretic separations.
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The DNA fragments are produced by the action of a restriction endonuclease
(Figure 19.4, page 462). We have seen that each type of restriction endonuclease cuts
DNA at a particular base sequence, as and when these occur along the length of the
DNA molecules. Consequently, the fragments are of different lengths. A series of
19
wells are cut close to one end of the gel and the gel is submersed in a salt solution that
conducts electricity. Then a small quantity of a mixture to be separated is placed in a
well. Several different mixtures can be separated in a single gel at the same time
(Figure 19.9). An animation of electrophoresis is available at www.dnalc.org/
resources/animations/gelelectrophoresis.html.

After separation the fragments are not immediately visible because they are tiny and
transparent. Their presence is identified either by staining or by the use of a gene probe.
Gene probes are single-stranded DNA with a base sequence that is complementary to
that of a particular fragment or gene whose position or presence is sought. The probe
must be made radioactive so that when the treated gel is exposed to X-ray film the
presence of that particular probe and the fragment it attached to will be disclosed.
Alternatively, the probe must have a fluorescent stain attached. It will then fluoresce
distinctively in ultraviolet light, thereby disclosing the presence of the particular
fragment or gene sought.
The alternative approach, demonstrated in Figure 19.9, involves the use of a stain to
locate the position of all DNA fragments.
Ethidium bromide DNA fragments fluoresce in short wave UV radiation

Methylene blue Stains gel and DNA but colour fades quickly
Nile blue A DNA visible in light and gel not stained
▲ Table 19.3 Stains used in electrophoresis
electrophoresis in progress
+
– electrode (carbon
–
fibre) – negative wells (DNA samples loaded
here after treatment with
restriction endonuclease)
power supply (battery –
maximum voltage 45 volts)
buffer solution
larger fragments
gel (of agarose or

polyacrylamide)
smaller fragments
positive
+ electrode
reservoir with
buffer solution
DNA electrophoretogram
–
subsequently:
DNA separates into bands of different sized fragments while
the potential difference is maintained (time depends on
voltage supplied) – the DNA fragments in the gel are made
Figure 19.9
visible, typically by the addition of a specific dye which
Electrophoresis – the penetrates and colours the bands of DNA fragments
separation of DNA
fragments +
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Barking Dog Art
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DNA microarrays
19 DNA microarrays are small, solid supports, typically made of glass,
silicon or nylon, each about the size of a microscope slide (Figure 19.10).
On to this surface, DNA probes that correspond to thousands of
different genes are attached in a regular pattern of rows and columns.
Each dot on the array contains a DNA sequence that is unique to a given
gene. The microarray is then used to measure changes in expression
levels of individual genes from cells under investigation.
The DNA that is to be tested originates as mRNA being expressed

by a particular cell. By the action of reverse transcriptase, this
mRNA is converted to cDNA. As the cDNA is being synthesised, it is
simultaneously linked to fluorescent dye. Then the DNA probes of the
microarray are exposed to this cDNA. Any complementary sequences
present will bind to the fixed probes. After this, the microarray is rinsed
free of any cDNA that has not hybridised and become bound. Finally,
the microarray is exposed to laser light that causes fluorescence where
there has been hybridisation between cDNA and a DNA probe, and the
results recorded. The brighter the light emitted, the higher the level of
expression of a particular gene in the cell from which the original mRNA
was obtained.
▲ Figure 19.10 Microarray analysis
machine with microarray being A full human genome microarray would have as many as 30 000
inserted spots. Others are made with clusters of genes that relate to particular
conditions, such as cancers, for example.
Analysis of a simple microarray
A DNA microarray might be used to investigate the level of gene expression in a
cancerous cell compared to that in a healthy (control) cell, for example. The steps to
such an investigation are:
1 mRNA is extracted from the cancerous cells and the control cells.
2 cDNA is created from both samples of mRNA, that from the cancerous cell is tagged
with a red fluorescent dye, while that from the control cell is tagged with green
fluorescent dye.
3 The two samples are then mixed together and hybridised to the microarray.
4 At each probe location the red- and green-labelled cDNA compete to bind to the
gene-specific probe.
5 When subsequently excited by laser light, each dot will fluoresce red if it has bound
more red than green cDNA. This will occur if that particular gene is expressed more
strongly in the cancerous tissue compared to the control tissue.
6 Conversely, a dot will fluoresce green if that particular gene is expressed more
strongly in the control tissue.
7 Yellow dots indicate equal amounts of red and green cDNA have bound to that spot –
meaning the level of expression is the same in both tissues.
The analysis is undertaken by a fluorescence detector (microscope and camera) to
produce a digital image of the microarray (Figure 19.11). From these data a computer
quantifies the red to green fluorescence ratio of each spot. Then the degree of difference
in expression of each gene between the cancerous and the control tissues is calculated.
Databases of nucleotide and amino acid sequences

Developments in bioinformatics (the storage, manipulation and analysis of biological
information via computer science) has led to the creation of powerful techniques that
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competitive hybridisation of
normal diseased red and green cDNAs
tissue tissue
extract mRNA
19
mRNA
reverse
transcribe with
green red
fluorescent microarray
label label
labelled dNTP
substrates

cDNA CTAGCGGT
GTACACGGTT
GTCAACGTCA
mix and hybridise to microarray CCCTAGCG
each spot of DNA

represents a
different gene
▲ Figure 19.11 Microarray analysis of differential gene expression
allow scientists to find similarities in nucleotide sequences and discover the function of
proteins among organisms of similar or different species.
Nowadays, data is collected around the globe and from different research groups. The
purpose of the resulting databases is to facilitate the sharing of this information, and
to allow the widest possible exploitation of a huge and ever-growing body of knowledge
and skills. A flavour of the scale of developments can be gleamed from the following
link to the 180 complete genomes sequenced: www.genomenewsnetwork.org/
resources/sequenced_genomes/genome_guide_p1.shtml
There are three nucleotide databases:
» GenBank hosted by the National Centre for Biotechnology Information (or NCBI).
» The European Nucleotide Archive or (ENA) hosted by the European Molecular
Biology Laboratories (EMBL).
» The DNA Data Bank of Japan or (DDBJ) hosted by the National Centre for Genetics.
Together they form the International Nucleotide Sequence Database Collaboration.
With the arrival of automatic DNA sequencing, these data banks have grown
exponentially.
The Human Protein Reference Database (HPRD) is a protein database. Most protein
sequences found in the database are the translation of the genes and genomes using
DNA sequencing. Once deposited in the databases, anyone in the world can easily
access the data. This sharing of data brings together researchers and clinicians and can
help, for example, with the accurate identification of disease-causing pathogens, or help
choose correct antibiotics, enabling faster treatment of diseases.
The benefits of these vast databases include:
» knowledge of the genome of parasites to aid research into disease prevention
» the ability to locate genes that are responsible for human genetic disorders, allowing
research into new treatments and genetic screening
» the ability to determine differences in base sequence of a gene in two species to
determine their evolutionary relationship.
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19.2 Genetic technology applied to medicine
19.2.1 explain the advantages of using recombinant human proteins to treat
disease, using the examples insulin, factor VIII and adenosine deaminase
19.2.2 outline the advantages of genetic screening, using the examples of breast
cancer (BRCA1 and BRCA2), Huntington’s disease and cystic fibrosis
19.2.3 outline how genetic diseases can be treated with gene therapy, using the
examples severe combined immunodeficiency (SCID) and inherited eye

diseases
19.2.4 discuss the social and ethical considerations of using genetic screening
and gene therapy in medicine
Starting point
★ Bioinformatics combines knowledge from gene mapping, protein analysis and
modern biotechnology in the service of science and society.
Recombinant human proteins and the treatment of disease

The production of a human protein by recombinant DNA techniques for the treatment of
disease was an early success in the development of genetic engineering. The human genes
for insulin were initially transferred to the bacterium, E. coli (and later more usefully to
yeast) and human insulin was made available to treat Type I diabetes (page 299).
Before genetically engineered human insulin was available for clinic use, insulin was
extracted and purified from the pancreases of pigs or cattle obtained from abattoirs after
their slaughter. Insulin from both animal sources was used to treat insulin-dependent
diabetes, although neither was exactly identical to human insulin.
Today, it is argued that genetically engineered human insulin has the following advantages:
» it is chemically identical to the body’s own insulin and triggers no immune response
as ‘foreign’ proteins tend to do when introduced into a patient’s body
» it is acceptable to patients who previously declined ‘pig’ or ‘cow’ insulin for religious
regions or because, as vegetarians, the use of animal products was unacceptable
» an immediate response is generated by the genetically engineered insulin because it
exactly ‘locks on to’ the insulin receptors in the relevant cell surface membranes; the
response brought about by insulin from other species is slower.
However, animal sources remain available and may be used in preference, if required.
Haemophilia, a rare genetically determined condition in which the blood fails to clot
normally, results from a failure to produce adequate amounts of blood proteins known
as clotting factors. These are glycoproteins normally released from cells at the site of a
haemorrhage (Figure 19.12). Today, haemophilia may be effectively treated by the
administration of the specific clotting factor a patient lacks. For example, haemophilia A
is due to a deficiency of functionally active factor VIII, normally the product of a gene
on the X chromosome. The human gene for factor VIII has been transferred to the
genome of cells obtained from hamster kidney tissue. These genetically engineered cells
are then grown in vitro, using an animal cell culture medium. The factor VIII protein is
then isolated, purified and administered to patients.
Severe combined immunodeficiency (SCID) is an inherited disorder due to absent or
malfunctioning T- and B-lymphocytes of the immune system. The result is a defective
antibody response. In SCID patients the immune system is so compromised it is effectively
absent, and victims are extremely vulnerable to infectious disease from a very early age.
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damaged blood vessel
19
exposed collagen fibres
and damaged endothelium
platelets collect, release clotting factor

platelet plug formed
adhere and release (e.g. factor VIII) from
– sufficient to block
SEM of blood clot minor breaks damaged tissue

showing meshwork of
fibrin fibres and trapped Ca2+ and vitamin K
local acting clotting factor
blood cells from plasma
hormones (e.g. factor VIII)
(prostaglandins)
prothrombin thrombin
(soluble protein (proteolytic enzyme)
in plasma)
fibrinogen insoluble
(plasma protein) fibrin fibres
trapped
fibrin fibres blood cells
constriction of damaged vessel blood clot
stabilised plug
prevents further blood loss
prevents entry of bacteria
▲ Figure 19.12 The blood-clotting mechanism
One form of SCID is due to a lack of the enzyme adenosine deaminase (AD), coded for
by a gene on chromosome 20. In the presence of a defective form of the gene, the substrate
of the enzyme this gene codes for accumulates in cells. Immature cells of the immune
system are sensitive to the toxic effects of this substrate molecule, and they fail to mature.
Now stem cells, harvested from the umbilical cord blood at birth, have been genetically
modified with the normal human AD gene (cDNA), introduced by retovirus. These GM
stem cells are then transfused into the neonate for successful gene therapy.
So, in summary, gene therapy is an application of genetic engineering with the aim
of supplying a missing gene to body cells in such a way that it remains permanently
functional, when this is thought safe and ethically sound. Gene therapy is a very recent, and
highly experimental, science. The steps to the process of gene therapy are discussed below.
Screening for genetic diseases

Genetic disorders are heritable conditions that are caused by a specific defect in a
gene or genes. Most arise from a mutation involving a single gene. The mutant alleles
that cause these conditions are commonly recessive. In these cases a person must be
homozygous for the mutant gene for the condition to be expressed. However, people
with a single mutant allele are carriers of that genetic disorder. Quite surprising
numbers of us are carriers for one or more such conditions.
An exception is Huntington’s disorder, due to a dominant allele on chromosome 4. In this
case, an individual will be affected even if they have a single allele (they will be heterozygous
for the defective gene). The disease is extremely rare (about 1 case per 20 000 live births).
A tendency to suffer from certain cancers also runs in families. An example is breast
cancer. In this case, there are two genes (known as BRCA1 and BRCA2), each with
one mutant allele, which can be inherited. There is also a 60 per cent probability
that the healthy allele will mutate at some stage, before the person reaches the age of
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50 years, thereby triggering breast cancer. Both BRCA1 and BRCA2 are natural tumour-
suppressing genes when present in the homozygous state.
19 Genetic disorders generally afflict about 1–2 per cent of the human population. These
include sickle-cell disease, Duchene muscular dystrophy, haemophilia (page 371), severe
combined immunodeficiency (SCID), and cystic fibrosis (CF) – on which we focus here.
The incidence of cystic fibrosis varies around the world. The available evidence suggests
that in Asia it is quite rare, but in Europe and the USA it occurs in roughly one newborn
person in every 3000–3500 births. In the UK, cystic fibrosis is the most common
genetic disorder. Here, one person in 25 is a carrier.
Causes of cystic fibrosis

Cystic fibrosis is due to a mutation of a single gene on chromosome 7, and it affects the
epithelial cells of the body. The CF gene is 180 000 base pairs long. This codes for a
protein known as CFTR, which functions as an ion pump (Figure 19.13). The pump
transports chloride ions across membranes and water follows the ions, so epithelia are
kept smooth and moist when this protein is present and working.
In cystic fibrosis, the most common mutation involves a deletion of just three of the
gene’s nucleotides and results in the loss of an amino acid (phenylalanine) at one
CFTR protein in situ in plasma membrane
liquid bilayer
of cell surface
membrane
* CFTR
protein
ATP binding
site 1 * * ATP
ATP binding
site 2
*be these sites must
activated for ion
channel to function
protein activated when ADP + P i
attachment of phosphate
(from ATP) occurs activation event –
the role of ATP ions
How CFTR regulates water content in mucus
1 when excess water is present 2 when too little water is present 3 in CF patient
Na+ pumped from mucus into cells and Cl– pumped from cells into mucus and CFTR channel absent or non-functional,
Cl– diffuses down electrical gradient – Na+ diffuses down electrical gradient – so Na + channel locked open – water is
water follows by osmosis from the mucus water follows by osmosis into the mucus continually removed from mucus by osmosis
mucus layer
epithelium
tissue fluid
Na+ Na+ Na+

Cl– Cl–
water water water
▲ Figure 19.13 The CFTR protein – a channel protein
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location along a protein built from almost 1500 amino acids in total. The mutated gene
Question
codes for no protein or for a faulty protein. The result is epithelium cells that remain dry
6 What do you
understand by the
and a build-up of thick, sticky mucus. 19
term mutant allele? The signs and symptoms of cystic fibrosis
The effects of faulty CFTR ion pumps are felt:
» in the pancreas – secretion of digestive juices by the gland cells in the pancreas is
interrupted by blocked ducts. Digestion is hindered.
» in the sweat glands – salty sweat is formed. This is used in the diagnosis of cystic

fibrosis.
» in the lungs – these become blocked by mucus and are prone to infection. This effect
is most quickly life-threatening if not treated promptly.
In adult patients, the membranes of epithelium cells in their reproductive organs are
affected too. Infertility frequently results. In women with cystic fibrosis, the mucus
naturally present in the cervix becomes a dense plug in the vagina, restricting entry
of sperm into the uterus. In men with cystic fibrosis, dense mucus in the sperm ducts
blocks these tubes, significantly reducing the sperm count when semen is ejaculated.
The process of genetic screening
We can now locate genes responsible for human genetic diseases, if we choose. This is
one outcome of the Human Genome Project. For example, the gene that codes for cystic
fibrosis (CFTR) was sequenced in 1989. This made possible the screening of human
cells for the presence of the mutated CFTR gene (Figure 19.14). So it is possible for
couples to be genetically screened to assess how likely they are to have children who
1 DNA extraction — cut with restriction endonuclease

cells e.g. from skin tissue or white mechanically broken up, then:
cells separated from a blood sample • cell debris removed by filtration and centrifugation
• cell membranes and nuclear envelopes broken down by incubation with detergent
DNA precipitated • proteins removed by incubation with protease enzyme restriction
in ice-cold ethanol so, DNA is freed from the nucleus, and from its histone ‘scaffolding’ endonuclease
‘cuts’ at a particular
restriction sequence of bases
DNA resuspended in aqueous,
DNA endonuclease
pH-buffered medium, and
incubated with restriction endonuclease
2 DNA fragments separated by electrophoresis 3 DNA transferred to nylon/nitrocellulose membrane

(Southern blotting)
Restriction endonuclease restriction sites
enzyme cuts DNA strands
into fragments of differing
length at the restriction sites, required gene
one of which will contain
the required gene.
restriction fragments
DNA fragments are separated by gel electrophoresis, using 4 DNA probe added – attaches to fragment
an agarose gel: complementary to CFTR gene
+ –
electrode
DNA is loaded into –
cavities cut in the
gel, then the
voltage is 5 DNA–probe complex detected – by X-ray film if
applied – + radioactive probe or by fluorescence under UV light
movement
electrode + agarose gel of fragments
negative charge on DNA (due to phosphate groups) causes

the fragments to move to the positive electrode (anode),
but the gel has a ‘sieving’ effect – smaller fragments move ▲ Figure 19.14 Steps involved in genetic screening for cystic
more rapidly than larger ones fibrosis
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Question will have cystic fibrosis (because both are ‘carriers’), for example. Alternatively, it is
possible for all members of a family group be offered screening where there is a history
19 7 How does the
development of a
of a particular condition.
Prenatal screening is used to test for the presence of a number of genetic conditions in
genetic disorder differ
for a person with a the unborn child. This allows the detection of:
single recessive allele » chromosome abnormalities such as Down syndrome (trisomy 21), trisomy 13 and
for cystic fibrosis trisomy 18. In the latter two abnormalities, only very rarely do affected infants
and a person with survive their first year.
a single dominant » single gene disorders, such as haemophilia, sickle cell anaemia and cystic fibrosis.
allele for Huntington’s » neural tube defects, such as spina bifida and anencephaly.
disorder?
Prenatal screening may be carried out by:
» chorionic villus sampling – undertaken at weeks 11–13 of the pregnancy, a sample
from the placenta is taken.
» amniocentesis – undertaken at weeks 15–20 of the pregnancy, the fetal cells in the
amniotic fluid are examined (Figure 19.15).
ultrasound
scanner
chorionic villus sampling –

withdrawal of a sample of the fetal
tissue part-buried in the wall of the uterus
uterus in the period 11–13 weeks
into the pregnancy; the tiny sample
is of cells that are actively dividing chorionic
villi vagina
and can be analysed quickly.
catheter inserted through vagina and

guided to collect chorionic villus tissue
sample with aid of ultrasound image
cervix catheter
amniocentesis – ultrasound
withdrawal of a sample of scanner
amniotic fluid in the period
15–20 weeks of gestation; uterus
the fluid contains cells from
the surface of the embryo
amniotic fluid
(with fetal cells)
syringe used to withdraw

placenta
amniotic fluid, the needle guided
with the aid of ultrasound image
vagina
cervix
▲ Figure 19.15 Prenatal screening

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EXTENSION
The outcome of screening – genetic counselling
19
The outcome of genetic screening frequently does
not necessarily allay a person’s (or their partner’s)
fears. They are likely to be referred to a genetic
counsellor. The role of the counsellor is to take a
detailed case history of the person and their
immediate family. A counsellor may then research

the family pedigree.
Reasons for referral to a genetic counsellor
» Screening has confirmed that one or both partners
are carriers.
» One or both partners have a relative with a genetic ▲ Figure 19.16 A genetic counselling session
disease.
possibility of further treatment in cases where a
» The partners are first cousins.
defective allele has been detected. There may be
» One or both partners belong to an ethnic group with
consequences for future health, life expectancy, the
an above-average risk of a genetic disease.
appropriateness of future education and training
» There is a history of earlier pregnancies ending in a and future employment. These are all issues where
miscarriage. information and reassurance may be needed.
» The partners are aged 38 or over. Sometimes, genetic conditions affect the chance of
In these cases people need to know the risk of their obtaining life insurance. The role of the counsellor is
offspring inheriting the defective allele or actually to provide information in a way which allows their
developing the disorder. One outcome may be the clients to make their own decisions.
Gene therapy
Gene therapy is a technique that attempts to use genes to treat or prevent disease by
inserting a gene into a patient’s cells instead of using conventional medicine or surgery.
Somatic gene therapy involves the transfer of a section of DNA to any cell of the body
that doesn’t produce gametes (so the effects of the gene therapy will not be passed on to
the patient’s children).
Vectors for gene therapy

» Liposomes are small lipid droplets that can be used to coat plasmids that contain
recombinant DNA. The lipid coating enables the droplet, with its recombinant DNA,
to cross cell surface membranes. Figure 19.18 overleaf shows how this technique has
been used, with mixed success, to transform epithelial cells in the lungs of human
sufferers of cystic fibrosis.
» Viruses, including retroviruses, have been used to transfer DNA into cells, as shown
in Figure 19.17. Since a retrovirus is an RNA virus, the enzyme reverse transcriptase
Figure 19.17 Gene liver (any tissue removed
will be regenerated)
therapy using a virus as 1 portion of liver is
vector removed from the body
2 broken into
individual cells
6 cells injected back into
liver via bloodstream`
5 liver cells with

healthy gene added
virus injects RNA

4 reverse transcriptase generates DNA, 3 healthy gene
which is added to chromosome added into retrovirus
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The cystic fibrosis gene codes for a membrane protein that occurs
widely in body cells, and pumps ions (e.g. CI–) across cell membranes.
19 part of DNA double strand

of chromosome 7
1 CFTR gene is cut and added to
a plasmid, using a restriction
endonuclease and then a ligase
bacterial plasmid
cystic fibrosis gene, functionally

a transmembrane regulator, so
known as the CFTR gene
CFTR gene and

bacterial plasmid
(negatively charged)
liposome
(enlarged)
liposome–DNA
complex
plasmid liposome
2 liposomes, tiny lipid membrane spheres (positively

charged), combine with DNA to facilitate entry
into lung cells across the cell surface membrane
3 liposome–DNA complex
administered to CF patient
as aerosol applied to lungs
via nose – in clinical trials
4.1 liposome–DNA complex fuses with epithelium cell

epithelium cell membrane of the lung
4.5 CFTR-coded ‘pumps’ become

installed in epithelium cell
membranes and normal mucus
4.2 plasmid with CFTR gene is formed
passes into cell and on
into the nucleus
4.4 CFTR mRNA passes to ribosomes
in cytoplasm and the CFTR-coded
4.3 here CFTR gene code protein is formed
is transcribed into mRNA
In recent clinical trials some 20% of epithelium cells of CF patients were temporarily modified (i.e. accepted the CFTR gene), but the effects were
relatively short-lived. This is because our epithelium cells are continually replaced at a steady rate, and in CF patients the genetically engineered cells
are replaced with cells without CFTR-coded pumps. Patients would require periodic treatment with the liposome–DNA complex aerosol to maintain
the effect permanently.
▲ Figure 19.18 Somatic gene therapy: supplying the healthy CFTR gene to the lungs
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that the virus carries has a key role in the insertion of recombinant DNA in the host
liver cells. A retrovirus has been used in the treatment of SCID. Adenovirus and
vaccinia virus have also been successful vectors, and the conditions treated include
inherited eye disease.
19
» Naked DNA. Genes have also been transferred by direct take-up of DNA from the
environment. The host cells have to be capable of taking up the DNA – a condition
described as ‘competent’. Calcium chloride treatment has proved to be one of the
best methods of preparing competent cells. The genetic diseases treated in this way
include SCID.

Social and ethical aspects of genetic engineering and gene
therapy
The benefits and hazards of gene technology
Questions Genetically modified organisms have been produced for specific purposes, relatively
quickly, where this proves possible. They offer enormous benefits However, geneticists
8 Suggest what are really producing new organisms when genes are transferred so there may be hazards
advantage would as well as benefits.
result from the
transfer of genes for
nitrogen fixation The benefits so far Hazards that have been anticipated
from nodules in » In addition to human insulin production by » Could a harmless organism such as
leguminous plants to modified E. coli, human growth hormone, the human gut bacterium E. coli be
cereals such as wheat. and blood clotting factor VIII have been transformed into a harmful pathogen
9 Occasionally produced by genetically modified bacteria. that escapes from the laboratory into
newspaper articles » Another application of genetic engineering the human population?
make criticisms of is bioremediation. This is the removal » Genes move between bacterial
genetic modification of toxic compounds, carcinogens and populations with time. Could the
of food organisms, pollutants, such as industrial solvents, antibiotic-resistance genes in plasmid
sometimes with contaminating ground waters and crude oil vectors become accidentally transferred
alarmist headlines. spills by genetically engineered bacteria into a pathogenic organism?
Search the web for that degrade these substances into safer » The accidental transfer of
articles that give molecules. The process is slow. herbicide resistance from crop plants,
differing views on » Sugar beet plants have been genetically such as sugar beet, to a related wild
this. Prepare the modified to be ‘tolerant’ of glyphosate plant and then on to other plants is
following to use in a herbicide applications. These plants are a possibility that could result in ‘super
discussion with your able to inactivate the herbicide when it weeds’ whose spread would be hard
peers. is sprayed over them, but the surrounding to prevent.
a a concise summary weeds cannot and are killed. (This is » Natural insecticidal toxin engineered
of the criticisms discussed further in this topic.) into crop plants, while an effective
frequently made,
» Similarly, natural resistance to attack by protection from browsing insects,
avoiding extremist
chewing insects has resulted from the might harm pollinating species such as
language or
addition of the genes for Bt toxin into bees and butterflies too.
unnecessary
crop plants (potato, cotton, and maize) by » The presence of the gene for the Bt
exaggeration
genetic engineering. This reduces the need toxin in the environment may lead to
b a list of balancing for extensive aerial spraying of expensive insects with resistance, too.
arguments in insecticides which are harmful to wildlife.
favour of genetic » There are well publicised anxieties
» There are ongoing attempts to use gene about food products from genetically
modification of
technology to treat genetic diseases, such engineered species. Might the food
food organisms
as cystic fibrosis (page 474) and severe become toxic or trigger some allergic
c a concise statement combined immunodeficiency (SCID). It is reactions? So far there has been no
of your own view hoped that some cancers may yield to this evidence of these problems.
on this issue approach in the future.
▲ Table 19.4 The benefits and potential hazards of gene technology
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The social implications of gene technology
19 Some of the social implications of gene technology are apparent from the list of benefits
and potential hazards in Table 19.4. We can summarise them as follows.
The advantages of gene technology for society may be:
» improved, cheaper medicines
» improved food supplies
» improved nutritional quality of foods
» a cleaner environment
» improved treatment of genetic diseases.
The disadvantages of gene technology for society may be:

» unexpected reductions in crop yields due to ecological disturbance
» farmers made dependent on specific varieties, needing fresh seed annually and
expensive fertilisers
» reduced natural biodiversity resulting in a reduced possibility of new varieties arising
» a reduced effectiveness of antibiotics as more bacteria become resistant.
Ethical issues in gene technology

Ethical implications depend on wider values. Ethics are the moral principles that we
feel ought to govern or influence the conduct of a society. Ethics are concerned with
how we decide what is right and what is wrong. Today, developments in science
and technology influence many aspects of people’s lives. This certainly throws up
increasingly complex ethical issues which we need to examine and respond to. Gene
technology is just one case in point.
There are important forces in our lives concerned with right and wrong in various ways,
but they are not themselves ethics (Table 19.5). After all, what is considered right and
what is considered wrong varies across the world.
The law Our laws are made by governments and may or may not be ethically
based. (In some cases, they may even only be a view held by a minority.)
Religion In our societies there are followers of different religions and of none, yet
ethics apply to us all.
Cultural norms Many of these are little more than ‘fashions’ that seemed acceptable at
one time and which may still be held uncritically.
Science While this may seek to give us an understanding of the origins of our world
and life, and how these work, it does not suggest how we should act.
Our feelings These are likely to be the product of our early environment, general
or conscience outlook and temperament, and our individual experiences.
▲ Table 19.5 Defining ethics by recognising what they are not
On the other hand, the principles we do use in coming to ethical decisions are identified
in Table 19.6. You can apply them to the issues that gene technology raises, after you
have read them, if you can accept them as comprehensive.
Regarding the ethics of gene technology, perhaps there are two broad issues that
societies need to address in deciding what developments they wish to fund.
» Is there an important over-riding principle to be held to, that humans should not
tamper with nature in a deliberate way? Are the changes in biodiversity and genetic
diversity that inadvertently flow from it completely beyond our current knowledge?
Alternatively, does all that we do influence and eventually change our environment
so our role is to see that our activities are conducted responsibly?
» To what extent is gene technology a costly technology that is mostly beneficial to the
health and life expectancy of wealthier people or perhaps to just those of developed
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nations? If the funds used for gene technology were made available for the more basic
problems of housing, health and nutrition in less developed countries instead, could
vastly more people benefit immediately? Alternatively, if we have the ability and
resources to bring about beneficial development, is it our duty to do so?
19
What does your group think?
Rights Human rights have been recognised and articulated, for
We have a duty to ensure example:
these » The United Nations Universal Declaration of Human Rights:

‘All human beings are born free and equal in dignity and
rights. They are endowed with reason and conscience and
should act towards one another in a spirit of brotherhood’.
» The European Convention on Human Rights, which
includes issues of security, liberty, political freedom and
welfare, and economic and group rights.
» In countries with a Bill of Rights written into their
constitution, as in the USA:
‘We hold these truths to be self-evident, …’.
Justice The principle that all should be treated equally; the idea
A principle to guide of fairness in our actions to each individual is considered
actions essential.
Utilitarianism The principle of the greatest good for the greatest
A belief that the overall number and with actions that generate minimal harm to
benefits should be greater others’ interests. In effect, this involves a cost–benefit
than the costs analysis.
Common good Where the life of a working, interacting community is
The core conditions that inherently good, then all actions should prosper and
are essential to the welfare support the common interest.
of all
Virtue Ethical actions necessarily respect and embody values
The placing of importance like truth, honesty, courage, compassion, generosity,
on a need to live a ‘good tolerance, integrity, fairness, self-control and prudence.
life’
Other criteria? Do you or your peers have any other criteria about which the
whole group can be convinced?
▲ Table 19.6 Ethical standards to apply in decision making
Ethical issues raised by genetic screening

The nature and application of ethical principles in decision making has just been discussed.
It is possible to abort a fetus that has been identified as carrying a defective gene. Genetic
counselling may result in ethical concerns for parents, medical personnel and for society
as a whole. Other ethical issues that screening and counselling may present include:
» Who should decide who may be screened or tested?
» What known disorders should be considered by the medical profession or society?
For example, should screening be available for disorders for which there is, as yet, no
known cure?
» Who should meet the substantial costs of screening, given the escalating cost of
public health provision, where this exists?
» Should the results be confidential? If not, who should have access to the information?
Should it be available to potential employers or insurance providers?
What other issues do you think are relevant?
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19.3 Genetically modified organisms in agriculture
19.3.1 explain that genetic engineering may help to solve the global demand for
food by improving the quality and productivity of farmed animals and crop
plants, using the examples of GM salmon, herbicide resistance in soybean
and insect resistance in cotton
19.3.2 discuss the ethical and social implications of using genetically modified
organisms (GMOs) in food production
Starting points
★ The ability to manipulate genes has many potential benefits in agriculture, but
the implications of releasing genetically modified organisms (GMOs) into the
environment are subject to much public debate in some countries.
Genetic engineering and improvements in quality and yield

The World Health Organization (WHO) has stated that hunger and related malnutrition
are the greatest threat to the world’s public health. Of the global population (currently
7.1 billion), some 870 million people suffer from chronic undernourishment. Most of
these people live in developing countries.
The growing issue of food shortage is due to several factors:
» The size of human populations – this currently increases by 75 million people per
year.
» The increasing wealth of populations in countries like China and Brazil. Growing
numbers of people who once obtained the bulk of their nourishment from a diet high
in grain (rice, wheat, maize) are increasing demand for meat and dairy products.
Animals reared intensively require grain. It takes 5 kilos of grain to produce a single
kilo of meat.
» Extreme weather conditions – climate change and water stress lessen agricultural
production.
» Small farmers, whose production may sustain the needs of many of the poorest
communities, have access to a shrinking land area. This is due to development of
industrial farming, demands imposed by urbanisation, transport and the growth
of cities, and the increasing use of land to grow alternative crops that supply raw
materials for industry and urban populations. Crops grown for biofuels is just one
example.
Genetically modified organisms have a part to play in worldwide improvement of
agricultural production by increasing quantity and nutritional value, and by reducing
loss due to pests and weed growth. However, the benefits arising from genetic
modification may be at a price that the poorest (and most undernourished) are mostly
unable to meet. There are urgent social and political factors to tackle too, in the battle
against hunger. Nevertheless, there have been significant successes achieved by genetic
Question modification.
10 Explain why any GM salmon

threat to honey bees
Wild salmon (Salmo salar) have been genetically engineered to include growth-hormone
and butterflies poses
such a problem to regulating genes from Chinook salmon of the Pacific ocean. This has resulted in a much
agriculture and faster growth rate, and one that is maintained all the year round, rather than just in the
horticulture. spring and summer when growth is fastest in wild and fish-farmed salmon. These GM
fish grow to market size in 18 months, rather than 3 years.
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Herbicide-resistant crops
Transgenic flowering plants may be formed using tumour-forming Agrobacterium. This
soil-inhabiting bacterium sometimes invades broad-leaved plants at the junction of stem 19
and root, forming a huge growth called a tumour or crown gall. The gene that induces
tumour formation occurs naturally in a plasmid in the bacterium, known as a Ti
plasmid. Useful genes may be added to the Ti plasmid (using restriction endonucleases
and ligase – see page 462), and the recombinant plasmid placed back into Agrobacterium.
Then a host crop plant can be infected by the modified bacterium. The gall tissue that
results may be cultured into independent plants, all of which also carry the useful gene.

The plant will then make the gene product, which will be useful to humans. Herbicide-
resistant soybean and other crop plants have been produced in this way (Figure 19.19).
Glyphosate is a powerful systemic herbicide. Once it has been absorbed by a green
plant it is translocated to all tissues and organs and inhibits an enzyme essential for the
production of amino acids. The outcome is that the whole plant dies. This enzyme is
absent from animals, so glyphosate has very low toxicity for animal life. On reaching the
soil, glyphosphate is inactivated and rendered harmless by soil bacteria.
The gene coding for the enzyme that inactivates glyphosphate has been identified
in these soil bacteria, isolated and then transferred to the crop plants (Figure 19.19).
These plants are now referred to as ‘herbicide-resistant’ because when the herbicide is
applied, the GM crop plant degrades the herbicide molecules and remains unharmed.
Meanwhile, glyphosphate is also absorbed by weeds and kills even the largest weeds,
including their extensive root systems.
glyphosate applied in solution

via a spray boom
herbicide is absorbed by
foliage it comes in contact
with and is transported all
around plants (systemic
herbicide)
GM sugar beet contains glyphosate inhibits enzymes

a gene for an enzyme for amino acid formation –
that inactivates quickly disrupting the weed
glyphosate (gene plant’s metabolism
obtained from naturally
occurring soil bacteria)
sugar beet grows free of

competition with weeds for
light and mineral ions
weeds die and decay
▲ Figure 19.19 Treatment of a herbicide-resistant sugar beet crop

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Benefits Dangers
19 » It eradicates weeds around herbicide-

resistant crops, where loss of yield due
» Fewer weed species on farmland and
longer periods without weeds growing
to competition with weeds is very high. breaks wildlife food chains.
» Glyphosate herbicide is transported all » Selection of a glyphosate-resistant crop
around the weed plant, killing even the plant ties the grower to one particular
largest weeds with extensive roots. herbicide product – choice is lost.
» Glyphosate inhibits an enzyme for the » Will genetically modified plant material,
production of essential amino acids when consumed by humans, release novel
in plants. This enzyme is absent from toxins or otherwise adversely affect

animals, so glyphosate has very low existing enzyme systems in the human
toxicity. digestive system?
» An average of five sprays of herbicide » Genetically engineered genes may be
are applied to sugar beet in conventional vectored in plasmids containing an
cultivation, whereas with GM beet a antibiotic-resistance gene to facilitate
maximum of three sprays (and normally processes in the lab. This latter gene
only one or two) are needed because of might be accidentally transferred to
the greater activity of glyphosate. human gut bacteria via food eaten.
» Cereals normally precede spring-sown » ‘Superweeds’ may develop by cross-
beet. Cereal stubble is an important pollination between herbicide-tolerant
source of food for bird life in autumn and crop plants and compatible weed species
winter. With glyphosate herbicide applied (fat-hen, sea beet and weed beet are
to GM beet being so effective, there is naturally occurring near relatives of
no need for weed control in stubble the sugar beet). Superweeds would be
preceding autumn – leaving wild birds’ difficult to eradicate from crops.
food sources available longer. » There is a possibility of cross-pollination
» Glyphosate herbicide provides good weed between GM crops and conventional
control, allowing cultivations by discs and organic crops. The maintenance of
or tines (conservation tillage) rather sufficient distance or the devising of
than by ploughing. These systems have effective barriers to prevent or reduce
fewer harmful effects on soil organisms, pollen transfers between crops may be
increase moisture, improve soil structure, difficult to achieve.
and reduce tillage costs. » If glyphosate herbicide droplets do reach
» Glyphosate herbicide is applied as large hedgerow plants (or further) their size
droplets from coarse nozzles, rather than and chemical activity in plants means
as a fine mist of tiny droplets that are they are more likely to do damage.
prone to drift on to surrounding habitats.
▲ Table 19.7 Benefits and potential dangers of growing glyphosphate-resistant crops
Insect-resistant crops
Natural resistance to attack by chewing insects has resulted from the engineering of the
genes for Bt toxin into crop plants such as cotton, reducing the need for extensive aerial
spraying of expensive insecticides, themselves harmful to wildlife.
While a natural insecticidal toxin, engineered into crop plants, is an effective protection
from browsing insects, it might also harm pollinating species such as bees and
butterflies. Also, the presence of the Bt gene in the environment may lead to insects with
resistance.
Ethical and social implications of GM organisms in food

production
In the description of the development of genetically modified organisms (GMOs)
presented in this topic, specific ethical, social and scientific issues have already been
raised (see pages 479–81).
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In preparing a paper for discussion with peers and your tutor, the issues can be
researched and your own opinion developed within the following framework:
» What social and legal controls does society need, to influence these developments? 19
» What effects may GMOs have on the environment and on surrounding, unrelated
species?
» What health risks are raised by GMOs, and what are their effects on human health?
» Who will have access to the technology, and how will scarce resources be allocated?
Because GMO technologies have been available for a relatively short while, some

possible long-term effects may not yet have emerged. Remember, ‘absence of evidence
is not evidence of absence’. The greatest dangers may be one or more that have not yet
emerged. On the other hand, if calculated risks are not taken, no progress is possible.
SUMMARY
» Genetic technology includes genetic engineering, » Genetically modified eukaryotes are harder to
DNA sequencing and genetic fingerprinting. produce. They carry two copies of a gene, unlike
Gene technology has applications in biotechnology, prokaryotes, so the engineering processes are
medicine and the pharmaceuticals industries, often more difficult. However, food plants with
agriculture and forensic science. Gene technology herbicide resistance, insect resistance or
generates many benefits for humans, but there are improved food value have been produced.
potential hazards, too, so gene technology raises » DNA sequencing involves the creation of genomic
ethical issues. libraries of the precise sequence of nucleotides
» Genetic engineering involves the transfer of genes in samples of DNA of individual organisms. The
from one species to another, possibly unrelated nucleotide sequence in the whole human genome
organism. Genes are transferred by inserting DNA was the product of the Human Genome Project.
into a vector, typically a plasmid, a tiny ring of Many other genomes have been completely
double-stranded DNA obtained from a bacterium. sequenced, too.
The gene and the vector are cut by means of » Electrophoresis is a process used to separate
the same restriction endonuclease, forming molecules such as proteins and nucleic acid
compatible sticky ends at the cuts. The gene and fragments (of either DNA or RNA) on the basis of
plasmid are then brought together and joined their net charge and size.
using the enzyme ligase. An alternative vector is » Genetic disorders are heritable conditions that
the nucleic acid of a virus. are caused by a specific defect in a gene or genes.
» Bacteria that have been genetically engineered Most arise from a mutation involving a single
to carry a new gene are identified by the use of gene. Genetic disorders affect about 1–2 per cent
plasmids that carry genes for resistance to two of the human population and include sickle cell
antibiotics, known as R-plasmids. Alternatively, a anaemia, haemophilia and cystic fibrosis. It is
fluorescent marker is used. possible that the symptoms of a genetic disorder
» For a gene to be expressed (transcribed into like cystic fibrosis may eventually be overcome
messenger RNA), a promoter normally needs to by gene therapy. The Human Genome Project
be attached and activated. One example is the lac has made it possible to screen for the presence
promoter mechanism present in certain bacteria. of the mutant cystic fibrosis allele. Consequently,
» A gene may be constructed from the messenger affected people and their relatives may be referred
RNA that it codes for, using the enzyme reverse to a genetic counsellor whose role is to take a
transcriptase. Alternatively, copies of genes detailed case history and to provide information
may be built up from nucleotides in the correct from which their clients can make choices.
sequence. This is worked out from the amino acid » Crop improvements are also attempted by genetic
sequence of the protein the gene codes for using engineering. Projects have included herbicide-
the genetic code. resistant soybean and insect-resistant cotton.
» Genetically modified bacteria are now used to The results have often been cautiously and even
make valuable products such as human insulin critically received, sometimes with possible
(for the treatment of diabetics), human growth good reasons. Genetic engineering remains
hormone and several other hormones and a technology with many opponents. Very few
enzymes of use in medicine, agriculture and other countries have approved genetically modified
industries. crops for commercial production.
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19 1 Haemophilia A and haemophilia B are common hereditary disorders of blood
clotting.
Haemophilia A is a sex-linked genetic disorder that affects approximately 1 in
20 000 males worldwide. It is caused by a recessive allele of a gene coding for a
clotting factor and results in excessive bleeding.
There is currently no cure, but symptoms of haemophilia can be treated with a
transfusion of a clotting factor to slow down the bleeding.
a State how genetic screening could reduce the number of cases of

haemophilia. [2]
b i Some genetic disorders can be treated with gene therapy.
Outline the aims of gene therapy. [2]
ii Suggest why haemophilia A is a suitable disorder for treatment with
gene therapy. [1]
c Haemophilia A and haemophilia B are caused by mutations in different blood
clotting genes, F8 and F9 respectively. Both disorders have been treated with
gene therapy involving the use of a vector.
i Table 1.1 shows the lengths, in kilobases (kb), of the F8 and F9 genes.
With reference to Table 1.1, suggest why gene therapy using the
F9 gene has been more successful than using the F8 gene. [2]
haemophilia gene gene length/kb

A F8 >8
B F9 1.4
▲ Table 1.1
ii Two frequently used vectors in gene therapy are compared in Table 1.2.
With reference to Table 1.2, explain the advantages and disadvantages of
using adenovirus rather than retrovirus as a vector. [3]
Feature Vector
Adenovirus Retrovirus
Genetic material of virus Double-stranded DNA Single-stranded DNA
Expression of inserted High gene expression gGene expression in
gene dividing cells only
Host immune response High Low
to virus
▲ Table 1.2
[Total: 10]
2 In humans, the gene RPE65 encodes a protein responsible for regenerating visual
pigment in rod and cone cells after they have been exposed to light. A recessive
allele of this gene causes impaired vision from birth, progressing to complete
blindness in early adulthood. This condition is called LCA.
In 2008, trials were carried out into the possibility and safety of treating LCA
using gene therapy.
a Suggest and explain why LCA is suitable for treatment using gene therapy. [3]
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b Six adults with this condition were used in the study. Genetically modified
adenoviruses (a type of virus that can cause respiratory infections) were used
as vectors.
The vectors were injected beneath the retina of one eye of each of the
19
participants.
Suggest two ways in which the genome of the adenoviruses used as vectors
would differ from that of normal adenoviruses. [2]
c Improvements were found in the vision of all the participants, but the small
number in the trials made most of these improvements not statistically
significant.

Suggest why these trials were designed to include such a small number of
participants. [2]
[Total: 7]
(Cambridge International AS and A Level Biology 9700 Paper 41 Q5 Oct Nov 2011)
3 a Four naturally occurring enzymes make possible the genetic
engineer’s activities. List these enzymes, their sources, and the
reaction they catalyse. [8]
b In the in-vitro synthesis of human insulin, a copy of the gene has been
made by first isolating mRNA from human pancreatic tissue. Outline
the steps that this process involves. [6]
c Explain the advantages gained by:
i Making the insulin gene from mRNA compared
to obtaining genes directly from relevant chromosomes. [3]
ii The choice of insulin obtained by genetic engineering for the treatment
of diabetics, compared to the use of insulin from animal sources. [3]
[Total: 20]
4 a Give an illustrated account of the separation of DNA fragments by
electrophoresis. [6]
b Explain:
i The nature and significance of ‘variable number tandem repeat’
sections of chromosomes in DNA fingerprinting.
ii The steps in the production of a DNA profile. [10]
c Outline the diverse applications of DNA profiling in science and society. [4]
[Total: 20]
5 a Outline the steps to crop improvement by genetic modification with
reference to canola sugar beet crops and herbicide resistance.
b Identify both the potential benefits of genetic engineering of food crops for
agricultural production and the possible hazards that may arise, illustrating
your answer with reference to current examples.
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Answers
Answers
1 Cell structure achieved in transmission electron microscopy to

observe cell ultrastructure – in suitably prepared
1 Transfer of energy (respiration), feeding or nutrition, specimens.
metabolism, excretion, movement and locomotion, 9 Staining is necessary to provide contrast between
responsiveness or sensitivity, reproduction, growth and the cytosol and the nucleus in an otherwise more or
development less transparent cell. The nucleus can then be seen.
2 a) 1 mm = 1000 μm Ribosomes, however, are too small to be detected by
Since 1000 ÷ 100 = 10, 10 cells of 100 μm will fit light microscopy.
along 1 mm. 10
b) The drawing of E. coli is 64 mm in length. cell wall cell surface
Its actual length is 2.0 μm. membrane
cytoplasm
Therefore, magnification = 64 × (1000 ÷ 2) tonoplast
= × 32 000 large central
vacuole
3 Length of cell is 80 mm = 80 000 μm.
nucleus with
Magnification = 400 nuclear envelope
Actual length is 80 000 / 400 = 200 μm. (a double membrane)
with nuclear pores
+
4 Magnification is × 60 (6 × 10) nucleolus and chromatin
5 See ‘The magnification and resolution of an image’, chloroplast
page 9. (double membrane
surrounds this organelle,
6 a) 7.3 μm b) 2.7 μm which contains grana
and stroma)
7 Feature Plant cells Animal cells starch grain within
the chloroplast
Cell wall Cellulose cell No cellulose cell (cytoplasm contains ribosomes,
wall present walls Golgi apparatus and mitochondria –
not visible)
Chloroplasts Many cells No chloroplasts;
contain animal cells 11 Cells vary greatly in size and in degree of specialisation
chloroplasts, cannot of structure associated with their various functions.
site of photosynthesise
12 See ‘ATP – the universal energy currency’ pages 242–3.
photosynthesis
13 a) A cell wall is characteristic of plant cells. It is
Permanent Large, fluid- No large
entirely external to the cell, surrounding the cell
vacuole filled vacuole permanent
surface membrane. The wall is not an organelle.
typically present vacuoles
Plant cell walls are primarily constructed from
Centrosome No centrosome A centrosome cellulose, an extremely strong material. When
present outside a growing plant cell divides, a cell wall is laid
the nucleus down across the old cell, dividing the contents.
Carbohydrate Starch Glycogen This primary cell wall has more layers of cellulose
storage added, forming the secondary cell wall. In some
product plant cells the secondary layers of cellulose become
very thick indeed. Cell walls are absent from
8 The electron microscope has powers of magnification
animal cells. Prokaryotes have cell walls, but they
and resolution that are greater than those of an optical
are chemically different from those of plants.
microscope. The wavelength of visible light is about
500 nm, whereas that of a beam of electrons used is The cell surface membrane is the membrane that
0.005 nm. At best the light microscope can distinguish surrounds and contains the cytoplasm of all cells. It
two points which are 200 nm (0.2 μm) apart, whereas is constructed almost entirely of protein and lipid.
the transmission electron microscope can resolve The lipid of membranes is phospholipid, arranged
points 5 nm apart when used on biological specimens. as a bilayer. The proteins of cell surface membranes
Given the sizes of cells and of the organelles they are globular proteins which are buried in and
contain, it requires the magnification and resolution across the lipid bilayer, with most protruding above
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the surfaces. The whole structure is described as a cytoplasm, DNA not supported by histone protein.
Answers
fluid mosaic. See Figure 4.3, page 83. Cell wall of peptidoglycan (long molecules/
b) See page 15. polymers of amino acids and sugars). Membranous
c) See page 15. organelles absent from cytoplasm. Protein
d) See Table 1.3, page 24. synthesised in small ribosomes (70S).
e) See page 19.
4 a) The complete range of organelles in a eukaryotic cell.
f) See Figure 1.13, page 15.
b i) ×60
ii) 10
END OF TOPIC QUESTIONS iii) The ability of the microscope to separate small
These answers are for guidance only. They do not represent objects which are very close together. Resolution
the full response required by questions in the examination. is determined by the wavelength of the light
Cambridge Assessment International Education bears no used. For the light microscope it is about 2 µm.
responsibility for the example answers to questions taken from
its past question papers which are contained in this publication.
1 a) Ribosome; lysosome; mitochondria; nucleus
b) Points of exit for messenger RNA, transcribed 1 Non-organic forms of carbon are found in the
from the DNA of chromosomes and on their way biosphere as carbon dioxide in the atmosphere;
to ribosomes for involvement in the translation dissolved in fresh and sea water as hydrogencarbonate
process and peptide formation. ions and as carbonates, e.g. calcium carbonate and
c) i) Free in the cytoplasm and attached to the magnesium carbonate, in the shells of non-vertebrate
surface of endoplasmic reticulum (forming animals, mostly marine but some of fresh water and
rough endoplasmic reticulum). terrestrial habitats, and as chalk and limestone rocks,
ii) In the cytoplasm they are concerned with the which are formed from fossilised shells.
formation of peptides with roles within the cell; 2 Carbon atoms are able to react with each other to form
attached to the surface of endoplasmic reticulum extended chains (straight or branched chains or rings).
they are concerned with the formation of peptides
The four covalent bonds of carbon atoms form a regular
for export beyond the cell surface membrane.
tetrahedron shape. If there are different groups attached
d) Smooth endoplasmic reticulum → vesicles → via
to each of the four bonds around a carbon atom then
the Golgi apparatus or directly to sites within the
there are two different ways of arranging the groups.
cell where lipids are required.
e) Nucleus, mitochondria and chloroplasts Carbon atoms form covalent bonds with other atoms,
f) i) Intuckings of the inner membrane of the such as oxygen, hydrogen, nitrogen and sulfur,
mitochondrion forming different groups of organic molecules with
ii) Increased surface area that houses the ATP distinctive properties.
synthesizing machinery (ATPase) Carbon atoms can form more than one bond between
g) Phagocytic cells such as macrophages, since here them. Carbon may share two pairs of electrons to form
bacteria and cell debris that have been taken into a double bond.
the cytoplasm are broken down by hydrolytic 3 See page 39 and Figure 2.10.
enzymes released from lysosomes. 4 See pages 39–42, particularly Figure 2.13.
2 This is a self-assessment exercise – check your answer 5 A polymer is a large organic molecule made of
by referring to Figures 1.10, 1.15 and 1.17, pages 11, repeating subunits known as monomers, chemically
17 and 18. combined together. Among the carbohydrates, starch,
3 a) The resolution of a high-quality light microscope glycogen and cellulose are all polymers built from a
is insufficient to expose the detailed structure of huge number of molecules of glucose (the monomer,
the cytoplasm of (for example) a bacterial cell, combined together in different ways in the three,
so the discovery of the absence of a nucleus and distinctive polymers).
of almost any sort of organelles came only from 6 See page 46.
analysis of electron micrographs of bacteria.
b) Literally, ‘prokaryote’ means before or without a 7 ‘R’ represents the remainder of the molecule; it has little
nucleus; ‘eukaryote’ means ‘good’ nucleus. or no effect on the chemical properties of the molecule.
c) Diagram must show and label: peptidoglycan 8 Given the naturally occurring pool of 20 different
cell wall, lack of membrane-bound organelles in types of amino acids, in a polypeptide of only 5 amino
cytoplasm, naked circular DNA, 70S ribosomes. acid residues there can be 205 different types of
d) Cells are extremely small, typically about 1–5 µm polypeptide, or 3 200 000.
in diameter. Nucleus absent, circular DNA helix in
489

In a polypeptide of 25 amino acid residues there can d) The test with Benedict’s solution is shown in
Answers
be 2025 different types. Figure 2.6. The result would be a brick red
In a polypeptide of 50 amino acid residues there can be precipitate of copper(i) oxide.
2050 different types. A polypeptide of more than 50 amino e) Collagen is the most abundant structural protein
acid residues is, by convention, called a protein. in animals in general, found in skin, tendons,
cartilage, bone, teeth and the walls of blood
So, there is virtually almost unlimited structural
vessels; it also forms the cornea of the eye.
variation possible in the proteins of cells. Remember, as
f) See Figure 2.25, page 53.
the sequence of amino acid residues changes, so does
the structure and properties of the resulting protein. 3 This is a self-assessment exercise – check your answer
by referring to Figure 2.27, page 56. The text that
9 See page 38 and Figure 2.19, page 48.
follows the diagram explains the properties of water and
10 See Figure 2.22, page 51. their significance, which are summarised in Table 2.2.
11 The term macromolecule means ‘giant molecule’. We 4 a) See the top part of Figure 2.20, page 49.
have seen that polysaccharides (e.g. cellulose) and b) Egg white solution: contents would be purple,
proteins (e.g. lysozyme) are made up of vast numbers indicating the presence of protein (peptide bonds).
of repeating smaller molecules (glucose, in the case of Starch solution: contents would be blue, the colour of
cellulose; different amino acids in the case of proteins). alkaline copper(ii) sulfate in the absence of protein.
Lipids, on the other hand, are composed of triglycerides c i) The long chain of amino acids in its molecule.
– relatively much smaller molecules. However, as these Proteins differ in the variety, number and order
are hydrophobic, they may clump together and give the of these amino acids. In the living cell, the
appearance of being huge molecules. sequence of amino acids in the polypeptide chain
12 In ionic bonding, atoms gain or lose electrons to is controlled by the coded instructions stored in
form positive or negative ions that have a stable the DNA of the chromosomes in the nucleus.
arrangement of outer electrons. In covalent bonding, ii) The structure that develops when parts of the
electrons are shared between atoms. polypeptide chain take up a particular shape,
13 In gases, molecules are widely spaced and free to move immediately after formation at the ribosome.
about independently. In liquids, molecules are closer Parts of the chain become folded or twisted,
together. In the case of water, hydrogen bonds pull the or both, in various ways. Two major structural
molecules very close to each other, which is why water forms are common. Part or all of the peptide
is a liquid at the temperatures and pressure that exists chain becomes coiled to produce an α-helix or
over much of the Earth’s surface. As a result, we have a folded into β-sheets. These shapes are permanent
liquid medium which life exploits. and are held in place by hydrogen bonds.
iii) The tertiary structure of a protein is the
END OF TOPIC QUESTIONS precise, compact structure, unique to that
These answers are for guidance only. They do not represent protein that arises when the molecule is further
the full response required by questions in the examination. folded and held in a particular complex shape.
Cambridge Assessment International Education bears no This shape is made permanent by four different
responsibility for the example answers to questions taken from types of bonding, established between adjacent
its past question papers which are contained in this publication. parts of the chain.
iv) The quaternary structure arises when two or
1 a) i) A – (a)glucose; B – fructose more proteins are bound together, forming
ii) glycosidic a complex, biologically active molecule.
iii) hydrolysis Haemoglobin consists of four polypeptide
b) Answers may include: sucrose is not a reducing chains held around a non-protein haem group.
sugar; there are no reducing sugars present; d) Hydrophobic interactions, disulfide bonds and
sucrose is not hydrolysed to monosaccharides/ ionic bonds – see Figure 2.22, page 51.
reducing sugars.
2 a) Giant molecules are known as macromolecules.
Chemically they are polymers, made by linking 3 Enzymes
together similar building blocks called monomers, 1 Enzymes work by binding to their substrate molecule at
e.g. polysaccharides (built from monosaccharide a specially formed pocket or crevice in the enzyme –
monomers) and proteins (built from amino acids). the active site. Most enzymes are large molecules and
b) Hydrolysis of cellulose gives the monosaccharide the active site takes up a relatively small part of the
glucose. Hydrolysis of collagen gives the amino acids total volume of the enzyme molecule. Nevertheless,
– glycine, typically with proline and hydroxyproline. the active site is a function of the overall shape of the
c) See Figure 2.13, page 42.
490

globular protein and, if the shape of an enzyme changes proteins. The blood is held at a pH of between 7.35
Answers
for whatever reason, the catalytic properties may be lost. and 7.45. pH is very important in living organisms
2 a) A catalyst is a substance that alters the rate of a because it affects the shape of enzymes, almost all
chemical reaction, but remains unchanged at the end. of which are proteins. For the same reasons, buffers
b) Inorganic catalysts are often used in enzyme experiments.
Enzymes
6 a) See Figure 3.14, page 73.
Typically a metal, such Typically made of
b) See Enzyme concentration, page 73.
as platinum, in a finely- protein
divided state, e.g. as
platinised mineral wool
Able to withstand high Protein is easily These answers are for guidance only. They do not represent
temperatures, high denatured by high the full response required by questions in the examination.
pressures and extremes of temperature, for Cambridge Assessment International Education bears no
pH, if necessary example responsibility for the example answers to questions taken from
Extremely specific
– most are specific 1 a) i) Hydrolysis
to one type of ii) At boiling point the enzyme is denatured and
substrate molecule this stops the reaction.
b) As the concentration of sucrose increases the
3 a) 100 initial rate
actual rate rate of the reaction increases though after a
90 concentration of about 30 g dm−3 the rate increases
volume of CO2 produced / cm3
80 more slowly until it reaches a plateau of 11.6

70
arbitrary units at about 80 g dm−3.
60 At low concentrations the substrate sucrose is
50 the limiting factor. There are not enough sucrose
40
molecules to bind with the active sites on the
enzyme. At higher concentrations, the enzyme
30
concentration is the limiting factor since all the
20
active sites on the enzyme will be occupied.
10
2 A activation energy B induced fit
0
0 20 40 60 80 100 120 140
C globular D extracellular
time of readings / s
E Michaelis–Menten constant (K m)
b) 96/40 = 2.4 cm3 s−1 3 a) Answers might include: bringing the reactants
closer together, enabling the bonds to be broken or
4 Pre-incubation is required to ensure that when the made more easily, causing the transfer of charges
reactants are mixed the reaction occurs at the known, to happen more easily.
pre-selected temperature. b) i) Answers should include some of the following
5 a) pH is a measure of the acidity or alkalinity of a (both qualitative and quantitative descriptions
solution. (Strictly, pH is a measure of the hydrogen to be included): the concentration of PABA
ion concentration.) A buffer solution acts to resist increases with time for all concentrations of
any change in pH when the solution is diluted or if the inhibitor; for the start of the reaction (at
a little acid or alkali is added. Many buffers used in between 2 and 3 minutes), the rate of reaction is
laboratory experiments contain a weak acid, such very similar for all concentrations of inhibitor;
as ethanoic acid (vinegar) and its soluble salt (e.g. increasing the concentration of inhibitor causes
sodium ethanoate). In this case, if acid is added, the rate of reaction to proceed more slowly/the
the excess hydrogen ions are immediately removed concentration of PABA produced is less. For
by being combined with ethanoate ions to form example, for use of data: when no inhibitor is
undissociated ethanoic acid. Alternatively, if alkali present the concentration of PABA produced is
is added, the excess hydroxyl ions immediately 1 µm after 10 minutes, 2.1 µm at 20 minutes,
combine with hydrogen ions forming water. At the 2.8 µm at 30 minutes, 3.3 µm at 40 minutes,
same time, more of the ethanoic acid dissociates, 3.9 µm at 50 minutes, 4.5 µm at 60 minutes.
adding more hydrogen ions to the solution. The This compares with the following when 30 µm
pH does not change in either case. of inhibitor is present: 0.5 µm at 10 minutes,
b) In the body of the mammal, the blood is very 0.75 µm at 20 minutes, 1.1 µm at 30 minutes,
powerfully buffered by the presence of a mixture of 1.2 µm at 40 minutes, 1.3 µm at 50 minutes,
phosphate ions, hydrogencarbonate ions and blood 1.2 µm of PABA produced at 60 minutes.
491

The greatest reduction in amount of PABA b) Hydrogen ions enter the gelatin blocks by diffusion
Answers
produced with inhibitor present is the amount and there cause the observed colour change.
after 60 minutes with 1 µm inhibitor (4.2 µm) Relatively large blocks (the 10 × 10 × 10 mm cubes)
compared with 3 µm present (2.9 µm); the have a low SA / V ratio so little of the interior
concentration of PABA produced is similar when matter is close to the external environment and the
1 µm inhibitor and no inhibitor present; after diffusion path is a long one. Here, colour change is
about 25 minutes the concentration of PABA slowest. The reverse is true of the smallest gelatin
increases approximately linearly with time for blocks (the 2.5 × 2.5 × 2.5 mm cubes).
all concentrations of inhibitor. 5 Compare Figures 4.10 and 4.11, pages 89-90. The
ii) Answers may include: use different (low and difference is the mechanism of the permeability of the
high) concentrations of substrate, with and membrane transversed; in facilitated diffusion this is due
without inhibitor present for all concentrations. to the properties of the substance that passes – it triggers
All other variables constant. Analyse results the opening of pores through which diffusion occurs.
(draw graph of results): if the effect of the 6 Water can diffuse cross a partially permeable
inhibitor is inversely proportional to the membrane and so can some solutes, but not others.
substrate concentration, then inhibitor is
7 The concentrated solution of glucose (where the
competitive; inhibitor is non-competitive if a
concentration of free water molecules is low) will
decrease in Vmax or no change in K m is seen.
show a gain of water molecules at the expense of the
dilute glucose solution.
4 Cell membranes and transport A ‘net’ gain of water molecules refers to the fact that
1 In periods of seasonal or prolonged low temperature, very many more water molecules diffuse into the
the proportion of unsaturated fatty acids in the plant concentrated solution than diffuse out.
cell membranes can be expected to increase. 8 The water potential of the jam is much lower than that of
2 A lipid bilayer is shown in Figure 4.2 (page 82). In the the fungal cytoplasm. A rapid net outflow of water occurs
presence of sufficient lipid, molecules of lipid arrange from the fungal hyphae, inactivating the fungal spore.
themselves as a bilayer, with the hydrocarbon tails 9 a) The dilute sucrose solution
facing together. This latter is the situation in the cell b) The concentrated sucrose solution
surface membrane. c) The solution with the lower water potential
Several organelles of eukaryotic cells have a double (concentrated sucrose solution)
membrane, including chloroplasts and mitochondria, 10 a) The dilute solution of glucose
in which there are present an outer and an inner b) The dilute solution of glucose
membrane, both of which consist of lipid bilayers. c) The concentrated solution of glucose
So an important difference between a lipid bilayer 11 More water molecules will diffuse in than out.
and a double membrane lies in the number of lipid Ultimately the integrity of the cell surface membrane is
bilayers present. threatened and survival of the animal cell is not ensured.
3 a) In a plant cell, however, as uptake of water continued
the cell would become extremely turgid.
Dimension/mm 1 × 1 2×2 4×4×4 6×6×6
12 Uptake of ions is by active transport involving
×1 ×2
metabolic energy (ATP) and protein pumps located in
SA/mm2 6 24 96 216 the cell surface membranes of cells. As with all aspects
Volume/mm3 1 8 64 216 of metabolism, this is a temperature-sensitive process
SA/V ratio 6/1 24 / 8 96 / 64 = 216 / 216 and occurs more rapidly at 25°C than it does at 5°C.
=6 =3 1.5 =1 Ions are transported across the membrane by specific,
dedicated protein molecules. Because there are many
b) Plot the graph of SA/V using an Excel spreadsheet.
more sodium ion pumps than chloride ions pumps,
c) As a cell increases in size the SA/V decreases.
more of the former ion is absorbed.
d) As a cell increases in size diffusion becomes
progressively less efficient as a mechanism for removal 13 Phagocytic cells of the lungs and of the airways serving
waste, such as CO2 from the interior of the cell. the lungs, engulf bacteria, bacterial spores and dust
particles – in fact, any small particles of foreign matter
4 a) that reach those surfaces, rendering them less harmful.
Dimensions/mm SA/V ratio
10 × 10 × 10 600 / 1000 = 0.6 14 a) See The cell surface membrane, pages 81–6.
b) See Figure 4.7, page 87.
5×5×5 150 / 125 = 1.2
c) See Figure 4.15, page 94.
2.5 × 2.5 × 2.5 37.5 / 15.6 = 2.4 d) See Movement by bulk transport, page 101.
492

END OF TOPIC QUESTIONS solution. In beaker 1 the external solution is less
Answers
negative (that is, there is little dissolved solute),
These answers are for guidance only. They do not represent
there is a net flow of water into the cell, the
the full response required by questions in the examination.
cytoplasm becomes expanded by water uptake and
Cambridge Assessment International Education bears no
the cell becomes fully turgid.
responsibility for the example answers to questions taken from
d) The external solution is more negative (that is,
there is much dissolved solute); there is a net flow
1 a) P is the protein on the right-hand side. Q is the of water out of the cell; the volume of cell solution
channel protein on the left. R is the sugar chain decreases; the cytoplasm pulls away from parts of
on the glycoprotein. S are the phospholipids on the cell wall (the cells are plasmolysed) and the
the lower surface. T are the cholesterol molecules strips decrease in length.
(the molecules with black heads within the e) The water potentials within and outside the cell
phospholipid layer). are the same, so there is no net movement of water
b) When solid matter, such as bacteria, is being molecules and no change in cell size.
taken in by endocytosis, part of the cell surface f) In osmosis the free water molecules can diffuse
membrane is pulled inwards and the surrounding but the solute molecules are retained on one side
cell surface membrane and cytoplasm bulge out. of the membrane.
The matter becomes enclosed in a small vesicle.
4 This is a self-assessment exercise – check your answer by
Energy from metabolism is then required to
referring to your own laboratory practical work record or
transport the vesicle across the membrane.
by discussions with peers and your teacher or tutor.
2 a) Different molecules (proteins and phospholipids)
are present in the membrane and are able to move.
b) Similarity: both composed of a phospholipid bilayer 5 The mitotic cell cycle
or both contain protein; difference the Davson– 1 See Chromosomes occur in pairs, page 107.
Danielli model has protein only on the outside
of the phospholipid bilayer, whereas in the fluid 2 The result of the opposite charges is a strong attraction
mosaic model, the proteins are on one surface or and high binding affinity between the DNA strand
embedded in the membrane; other molecules such as it wraps around the histone-protein core of the
as chloresterol are present in the cell membrane. nucleosome.
c) Active transport is the movement of ions or 3
molecules across the cell membrane against their Meiosis Mitosis
concentration gradient. Energy is required. There The products 2 identical 4 non-identical cells,
is a specific carrier protein or pump, which may cells, each with each with the haploid
undergo a conformational change as the molecule the diploid chromosome number.
or ion is transported. chromosome
d) Proteins become denatured at high temperatures number.
because the bonds involved in their tertiary or
The Produces Produces haploid cells.
quaternary structure are broken, and so they consequences identical Contributes to genetic
lose their shape. The effects this has on the cell and diploid cells. variability by:
membrane may include: their active site for significance
transport of substances across the cell membrane Permits » reducing chromosome
growth within number by half,
or for recognising antigens is no longer there,
multicellular permitting
so the cell membrane is damaged as it can no
organisms, fertilisation, and the
longer function correctly; the proteins may not fit
and asexual combination of genes
properly or at all in the cell membrane, thus the
reproduction from two parents;
cell membrane is no longer intact.
» permitting random
3 a) The contents of damaged cells are removed with assortment of
the minimum of exposure of the cells to water paternal and
prior to the experiment. maternal homologous
b) Samples of 10 strips are large enough to rule out chromosomes;
abnormal individual differences in a single strip » recombination
that might make the results unrepresentative. of segments of
c) The net direction of water movement is into or individual maternal and
out of a plant cell depending upon whether the paternal homologous
water potential of the cell solution is more or less chromosomes during
negative than the water potential of the external crossing over.
493

4 a) A haploid cell contains one set of chromosomes, molecule containing two or more nitrogen atoms
Answers
the basic set. in the ring, covalently bonded together. They are
b) i) For example, in the layer of cells forming derived from one of two parent compounds, purine
sperm, in the testes. (a double ring compound) or pyrimidine (a single
ii) For example, in the bone marrow where red ring compound).
blood cells are formed or in the generative An inorganic base is a substance that can accept a
layer of the skin at the base of the epidermis. hydrogen ion and so neutralise an acid. Strong bases
5 See Table 5.2 Common carcinogens known to increase are substances like sodium hydroxide. They are
mutation rates and the likelihood of cancer, page 115. ionised compounds.
6 46 × 2 = 92 2 The most likely reason why many replication forks are
7 a) See table under part (b). required in the replication of a single strand of DNA
Your pie chart should comprise sectors with the may be that there are (typically) 80 million base pairs
following angles at the centre: Prophase 252°, to be copied. A single replication fork would seem to
Metaphase 36°, Anaphase 18°, Telophase 54°. be inadequate.
b) 3 See Figure 6.12, page 132.
4 See Figure 2.20, page 49.
Stage of Percentage of Time taken by each
mitosis dividing cells step/minutes 5 RNA involved in transcription
Prophase 70 70 ÷ 100 × 60 = 42 messenger See Protein synthesis – the stages

Metaphase 10 10 ÷ 100 × 60 = 6 RNA (mRNA) Stage one: transcription, page 131.
Anaphase 5 5 ÷ 100 × 60 = 3 RNA involved in translation
Telophase 15 15 ÷ 100 × 60 = 9 messenger mRNA is now a linear molecule in the
RNA (mRNA) cytoplasm along which ribosomes
move, ‘reading’ the genetic code and
END OF TOPIC QUESTIONS transcribing the information into a
These answers are for guidance only. They do not represent linear sequence of amino acid residues
the full response required by questions in the examination. (= primary structure of the protein)
Cambridge Assessment International Education bears no transfer RNA See The stages of protein synthesis, Stage
responsibility for the example answers to questions taken (tRNA) two: amino acid activation, page 133.
from its past question papers which are contained in this
publication.
6 See also Figure 6.11, page 131 and Figure 6.18,
1 a) Mitosis occurs during growth when new cells are page 137.
formed to develop into the tissues and organs of a) Gly (glycine), Asn (asparagine), Pro (proline),
the animal and when cell divisions occur to repair Phe (phenylalanine), Val (valine), Thr (threonine),
or replace cells. His (histidine), Cys (cysteine)
b) The cell cycle is the sequence of events between b) CCT, TTA, GGA, AAA, CAA, TGA, GTA, ACA
one division of a cell and the next. c) See Triplet codes, codons and anticodons, page 135.
c) See Figure 5.5, page 112 (left-hand side) and
Table 5.1. END OF TOPIC QUESTIONS
d) See Figure 5.5, page 112 (right-hand side).
2 This is a self-assessment exercise – check your answer the full response required by questions in the examination.
by referring to the section headed ‘Cancer – diseases Cambridge Assessment International Education bears no
of uncontrolled cell division’ (pages 114–5), including responsibility for the example answers to questions taken
Figure 5.7. from its past question papers which are contained in this
3 a) i) [1 A]; 2 C; 3 E; 4 D; 5 B; 6 F publication.
ii) interphase; anaphase, prophase; anaphase;
[metaphase] 1 a) late interphase, before mitosis
b) i) hydrogen bonds
ii) Y as it is a single ring structure, a smaller
6 ucleic acids and protein
N molecule.
synthesis c) i) A change in the DNA sequence (nucleotide or
base pair), which then in turn causes a different
1 The nitrogenous bases are organic compounds. mRNA to be transcribed, this may lead to a
The carbon ‘backbone’ of nitrogenous bases is a ring different polypeptide being manufactured. This
494

may mean that the protein does not function or c) Following transcription, the mRNA leaves the
Answers
does not function correctly. nucleus through pores in the nuclear envelope
ii) Answers may include: cell growth is and passes to the ribosomes in the cytoplasm.
unchecked, leading to more frequent mitosis Amino acids in the pool available for incorporation
and shorter interphase. The cells will not are activated by combining with short lengths of
differentiate into the type of lung cells they transfer RNA (tRNA). There is a different tRNA
should become so their function within the for each of the 20 amino acids. One end of the
lung is not carried out, and the cancer cells will tRNA has a sequence of three bases called an
not be broken down as normal cells are when anticodon which is complementary to the codon
they reach the end of their life cycle. of the mRNA. The amino acid becomes attached to
2 a) The messenger RNA formed from the coding its tRNA by an enzyme in a reaction that requires
strand of the DNA will contain 12 000 ÷ 2 = 6 000 ATP. During translation, the polypeptide chain is
nucleotides. assembled as the ribosomes move along the mRNA
‘reading’ the codons from the start codon. While
Each amino acid is specified by a codon in the mRNA
held in position the amino acids are joined by
made up of three nucleotides, so the maximum
peptide bonds.
number of amino acids is 6000 ÷ 3 = 2000.
b) ‘start codon’ and ‘stop codon’
c) Codons: UUU UAU CAU AUU GUG ACG 7 Transport in plants
GAG AGC 1 The shape of the cellulose polymer allows close
Anticodons: AAA AUA GUA UAA CAC UGC packing into long chains (see Figure 2.13, page 42)
CUC UCG held together by hydrogen bonds. The cellulose
d) tRNAs are relatively short (compared with the fibres are laid down in porous sheets and have great
length of mRNA), but long enough to be folded tensile strength. The monomer from which cellulose
into the shape of a clover-leaf. There is a different is assembled, by a condensation reaction, is glucose,
tRNA for each of the 20 amino acids involved in of which green plants typically have an excellent
protein synthesis – each amino acid has its ‘own’ supply.
type of tRNA. 2 a)
At one end of each tRNA molecule is a site where compact flat and thin
the particular amino acid can be joined. The small medium large small medium large
other end of the tRNA molecule is folded into a dimensions/ 1×1 2×2×2 4×4 2×1 8×2 16 × 8
loop. Here, a sequence of three bases forms an mm ×1 ×4 × 0.5 × 0.5 × 0.5
anticodon. This anticodon is complementary to surface area / 6.0 3.0 1.5 7 5.25 4.4
the codon of mRNA that codes for the specific volume ratio
amino acid. b) As the size of an object increases, so does the

surface area. However, the increase is very much
3 a) D is uracil. E is adenine. F is ribose. G is
greater in a flat, thin object compared to in a
phosphate.
compact object.
b) Any three of the following:
c) The surface area/volume ratio decreases as the
mRNA DNA size of an object increases but the decrease is very
much greater in compact object than in flat, thin
1 The pentose sugar The pentose sugar is
objects.
is ribose deoxyribose
d) Movements of nutrients into an organism and of
2 Contains uracil Contains thymine but not waste products out of an organism by diffusion
but not thymine uracil alone is only likely to be possible in small
3 Consists of a Consists of a double organisms (effectively, unicellular organisms).
single strand strand, forming into a However it may be a possible mechanism for
helix transport in small multicellular organisms of a flat
4 No base pairing Base pairing thin shape.
5 Found in the Found in the nucleus
cytoplasm
6 Produced by Produced by semi-
transcription conservative replication
495

They are also very soluble and are easily leached
Answers
3 TS of a sunflower stem (low power) – plan diagram
away into ground water in heavy rain. By taking up
cortex epidermis nitrates whenever they are available (and storing
them in cells), plant growth can be maintained.
leaf trace b) Plant roots are metabolically very active and require
oxygen for aerobic respiration and ATP formation
(for ion uptake, for example). Waterlogged soil
lacks soil air and the essential gas, oxygen.
vascular
bundle 10 Cultivation and cropping of plants to supply food for
pith the market place involves the ‘harvesting’ of organic
matter (and the nutrient ions built into it during
growth). If the supply of essential minerals that plants
fibres require is not maintained in the soil, the productivity
xylem of the land will rapidly fall. Consequently, largely
phloem
scale: 10 mm cambium
soluble nutrients are added as artificial fertilisers
spread on the soil as granules at the time of peak crop
4 Your answer should refer to the features of their growth. Alternatively, farmyard manure is applied to
structure (see The movement of water through the the soil at the time of ploughing. This decays slowly
plant, pages 149–52, particularly Figure 7.8), their and releases nutrients more steadily.
intimate contact with the soil solution and to their 11 Mitochondria produce ATP (the energy currency
position on the growing roots. The significance of a molecule). ATP transfers energy to enable the active
gradient in water potential between soil solution and transport of solutes in the sieve tubes. The presence
the root cortex is explained in Uptake of water – the of mitochondria confirms that phloem transport is
roles of the root hairs (page 150). an active process, using energy transferred during
5 The casparian strip blocks the apoplast pathway of respiration.
water movement across the cortex at the endodermis. 12 a) The functioning of living cells (e.g. in the phloem
6 As temperature increases, evaporation of water from tissue) would be impaired as proteins were
the surfaces of the cells in the leaf increases. At the denatured and cell surface membranes disrupted.
same time, the movement of molecules of water is Translocation would stop. Water flow in the xylem
increased (their kinetic energy is raised), so diffusion vessels would be unaffected.
occurs more quickly. Also, as temperature increases, b) The concentration of sugar might be lower in a
the humidity of the air is decreased because warm air sieve tube near the base of the stem, if starch is
holds more water vapour. So the gradient in water being stored in the cells at that point.
vapour between the interior of the leaf and air outside 13 a) Sugar delivered by the phloem from the leaves is
is increased and diffusion of water vapour stored as starch (insoluble) on arrival. Many of
is enhanced. the ions absorbed from the soil are used in the
7 See The transpiration stream, pages 154–5. metabolism of the root cells or are carried to the
8 Transpiration is a direct consequence of plant stem and leaves in the xylem.
structure, plant nutrition and the mechanism of gas b) Sugars produced in the light in the chloroplasts
exchange in leaves. In effect, the living green plant is accumulate in the cells of the leaf before being
a ‘wick’ that steadily dries the soil around it. Put like translocated away to ‘sink’ sites.
this, transpiration is an unfortunate consequence of
plant structure and metabolism, rather than a valuable END OF TOPIC QUESTIONS
process. It means that a constant, adequate supply of These answers are for guidance only. They do not represent
water is critical to plant growth; if the water supply the full response required by questions in the examination.
fails, plants cannot move elsewhere, as animals tend Cambridge Assessment International Education bears no
to do. responsibility for the example answers to questions taken
9 a) Plant growth is dependent on a supply of chemically from its past question papers which are contained in this
combined nitrogen (for protein synthesis) of publication.
which nitrates are typically the most readily 1 a) Glucose and fructose are water soluble polar
available. However, nitrates are also taken up by molecules not lipid soluble, so cannot pass across
microorganisms and may be released in the soil at the lipid bilayer, and need to be transported across
times other that when plant demand is at its peak. the cell membrane.
496

b) Moves into companion cell: at X protons move into 2
Answers
Pulmonary circulation Systemic circulation
the companion cell by facilitated diffusion. Sucrose Carries deoxygenated blood Carries blood under high pressure
molecules are cotransported into the companion under high pressure from the from the left side of the heart to
cell with the protons, against the sucrose right side of the heart to the the all the body organs
concentration gradient. At Y the protons that are lungs
cotransported into the cell are actively transported Returns oxygenated blood under Returns deoxygenated blood
lower pressure to the left side of under lower pressure to the right
across the cell membrane out of the cell, against the heart side of the heart
the proton concentration gradient. They diffuse
Consists of pulmonary arteries Consists of aorta and arteries
into the cell wall. delivering blood to lungs, delivering blood to the body
Moves from the companion cell into the sieve tube capillary networks serving organs, capillary networks
the air sacs of the lungs, and serving all the tissues and cells
element: sucrose concentration is thus higher in
pulmonary veins carrying blood of the organs of the body, and
the companion cell. Sucrose diffuses down its back to the left side of the heart vena cava carrying blood back to
concentration gradient into the sieve tube element. the right side of the heart
c) Any two of the following: flowers, shoot (tip), 3 a) The velocity and pressure of the blood as it enters
leaves, stem, root (tip), seeds, bulbs, tubers, corms the aorta are both high, but as it is about to re-
2 a) See Figure 7.16, page 156. enter the heart the pressure is very low. However,
b) Any three of the following: humidity – affects the close to the heart, the velocity of the blood in the
rate at which water can evaporate from the leaf to veins is similar to that of the main arteries leaving
the external air; temperature – affects evaporation the heart. This is necessary to ensure adequate
of water from leaf surfaces through open stomata; venous return to balance the cardiac output.
air movement – affects removal of water vapour b) The blood speeds up on leaving the capillaries
from around open stomata, which affects the because the total cross-sectional area of the
gradient of water vapour between leaf interior and venules is much less than the capillaries. The total
external air; water supply to the plant – affects cross-sectional area of the venous system further
turgidity of guard cells, which controls opening decreases as venules join up to form the veins.
and closing of stomata. c) The velocity of the blood is at its lowest in the
c) A plant adapted to withstand drought. capillaries. Capillaries are the smallest blood vessels
d) See Table 7.2 and Figure 7.17, page 157 – referring but their total cross-sectional area is typically 800
in particular to cuticle thickness and leaf structure times greater than that of the aorta leaving the
features (i.e. the potential of the leaves to roll heart (diameter of about 25 mm). The slow blood
up and the position of the stomata) and the root flow in the capillaries allows for efficient exchange.
systems and their roles. 4 5 × 106 cells per mm3 is equivalent to 5 × 109 cells per
3 a) Water passes into the root hair from the soil litre.
by osmosis across the partially permeable cell So, in 5 litres (i.e. the whole body), there are
membrane. It then mostly travels to the cells of 5 × (5 × 109) = 2.5 × 1010 cells.
the cortex via the apoplast pathway (the free space If a red blood cell lasts for 120 days, divide the total
between the cellulose fibres in the cell wall, so number of cells by 120 to find how many, on average,
non-living tissue). Some also travels through the need to be replaced each day:
symplast pathway, through the cell cytoplasm.
Water enters cells through the cell surface 2.5 × 1010 ÷ 120 = 2 × 108 approximately
membrane by osmosis and diffuses through 5 a) The components of the blood that are not found in
the cytoplasm and the cytoplasmic connections tissue fluid are the blood proteins, mainly albumin,
between cells (plasmodesmata). and red blood cells and platelets. (White blood
b) To provide energy (ATP) for active transport of cells are found in the tissue fluid – see page 172).
ions against their concentration gradient. b) Tissue fluid Lymph
Urea Absent Present
8 Transport in mammals Respiratory

gases
Contains oxygen but
no carbon dioxide
Contains carbon
dioxide but no oxygen
1 For example, it means that blood cannot be directed Products of Present in abundance Reduced to products
digestion of lipid digestion –
to a respiratory surface immediately before or after
and with proteins in
servicing tissues that are metabolically active (and lymph draining from
so have a high rate of respiration). Rather, the blood the liver
circulates randomly around the blood spaces and Lymphocytes Very few or absent Present
blood vessels.
497

6 A fall of about 25 per cent 2 a) Endothelium (inner lining) of pavement epithelium:
Answers
7 These non-elastic strands keep the heart valve flaps • strong, thin, single layer of cells fitting together
pointing in the direction of the blood flow. They stop like jigsaw pieces
the valves turning inside out when the pressure rises • smooth inner surface that minimises friction
abruptly within the ventricles. • walls have tiny gaps between cells sufficient
to allow certain components of the blood to
8 a) The pressure in the aorta is always significantly
escape and contribute to the tissue fluid.
higher than that in the atria because blood is
b) See Table 8.1, page 170.
pumped under high pressure into the aorta and,
c) In a single circulation the blood passes through
during diastole and atrial systole, the semilunar
the heart once in every circulation but in a double
valves prevent backflow from the aorta. Meanwhile,
circulation it passes through the heart twice.
blood enters the atria under low pressure from the
This means there is no mixing of oxygenated and
veins and the pumping action of the atria is slight
deoxygenated blood so the blood that is circulated
compared to that of the ventricle, which generates
around the body has a higher concentration of
our ‘pulse’.
oxygen than would otherwise be possible.
b) Pressure falls abruptly in the atrium once
d Plasma Tissue fluid
ventricular systole is underway as atrial diastole
begins then. Mainly water Mainly water
c) The semilunar valve in the aorta only opens when Nutrients from the Nutrients from the gut or
the pressure in the ventricles exceeds that of the gut or liver liver
pressure in the aorta.
Excretory products Excretory products such as
d) At the end of systole, pressure in the ventricles is
such as urea urea
high. When ventricular diastole commences the
bicuspid valve will only open when pressure in the Proteins, mainly Few proteins can pass
ventricles falls below that in the atria. albumin; also through the capillary
e) About 50 per cent of the cardiac cycle is given over hormones and walls into the tissue fluid
antibodies so proteins, particularly
to diastole – the resting phase in each heart beat.
albumin, are largely absent
The heart beats throughout life and takes limited
rest at these moments. Red blood cells, No red blood cells, white
white blood cells blood cells or platelets are
and platelets present
e) vena cava → right atrium → right ventricle →
pulmonary artery → arterioles and capillaries of
the lungs → pulmonary vein → left atrium →
left ventricle → aorta → artery supplying arm →
responsibility for the example answers to questions taken
arterioles and capillaries serving the muscles
from its past question papers which are contained in this
3 This is a self-assessment exercise – check your answer
publication.
by referring to ‘Blood – the transport medium’ (pages
1 a) i) 0.24 s or 0.25 s 171–2), ‘Transport of oxygen and carbon dioxide’
ii) 0.08–0.09 s (pages 176–9) and ‘Translocation’ (pages 160–63).
b) Similarities: the nerve impulses in both
ventricles happen at the same time so that both
ventricles contract at the same time. Thus the 9 Gas exchange
LV pressure goes up at the same time as the RV
1 Factors affecting the rate of diffusion and their
pressure, and returns to its minimum pressure at
consequences are identified and explained in Table 4.1.
the same time.
2 Amount of oxygen in 1 litre of blood = 20 × 10 = 200 cm3
Differences: the RV pumps deoxygenated blood to
the lungs; the LV pumps oxygenated blood round Amount of oxygen in 1 litre of water = 0.025 × 1000 =
the lungs so the change in systolic pressure is 25 cm3
much greater for the LV, and it has a higher peak Therefore, 175 cm3 more oxygen is carried by a litre of
pressure. blood compared with the same quantity of water.
498

3
Answers
lumen of
bronchiole
lining of
columnar
epithelium
(goblet cells
are rare here)
smooth muscle
surrounding the
makes up the
bronchiole
bulk of the wall
are numerous
(cartilage is
alveoli
absent here)
4 About 10–15%. Land-living organisms obtain oxygen 7 Carbon dioxide is an acidic gas which, if it were
from the air, but diffusion within an organism occurs in to accumulate in the blood, would alter the pH of
solution, so the first step in oxygen uptake in the lungs the plasma solution. The normal pH of the blood is
is the dissolving of oxygen in the surface film of water at 7.4. For life to be maintained it must remain within
the respiratory surface. As a consequence, the respiratory the range pH 7.0–7.8. This is largely because blood
surface is kept moist and water vapour will evaporate as pH affects the balance of essential ions which are
gaseous exchange occurs. See Figure 9.6, page 192. transported in the plasma solution. Efficient removal
5 Gas exchange is the exchange of respiratory gases of respiratory carbon dioxide from the lungs is as
(oxygen and carbon dioxide) between cells of an important to life as efficient uptake of oxygen.
organism and the environment; cellular respiration
is the cellular process by which sugars and other END OF TOPIC QUESTIONS
substances are broken down to release chem ical These answers are for guidance only. They do not represent
energy for other cellular processes. Gas exchange is a the full response required by questions in the examination.
consequence of cellular respiration. Cambridge Assessment International Education bears no
responsibility for the example answers to questions taken
6
Feature Effects and consequences from its past question papers which are contained in this
Surface area A huge surface area for gaseous exchange publication.
of alveoli (Approximately 50 m2, about the area of 1 trachea; bronchi; bronchioles; alveoli
a doubles tennis court.)
2 The deoxygenated blood arriving in the lungs in
Wall of Very thin, flattened (squamous)
blood capillaries is low in oxygen (it has a lower
alveoli epithelium (5 μm thick) so the diffusion
pathway is short.
partial pressure of oxygen than the alveolar air)
but high in carbon dioxide (it has a higher partial
Capillary A network of capillaries around each pressure of carbon dioxide than the alveolar air). As
supply to alveolus supplied with deoxygenated
blood flows past the alveoli, gaseous exchange occurs
alveoli blood from the pulmonary artery and
draining into the pulmonary veins by diffusion. Both oxygen and carbon dioxide are
maintains the concentration gradients diffusing down their concentration gradients. Oxygen
of oxygen and carbon dioxide. dissolves in the surface film of water on the squamous
epithelial cells of the alveolar membrane, diffuses
Surface film Oxygen dissolves in the water lining the
of moisture alveoli and diffuses into the blood in across the endothelium of the capillary and into the
solution. blood plasma. In the red blood cells, the oxygen
combines with haemoglobin to form oxyhaemoglobin.
Elastic fibres Stretched during inspiration, they then
At the same time, carbon dioxide diffuses from the
in walls recoil, facilitating expiration.
blood into the alveolus and is exhaled from the lungs.
499

The blood (now oxygenated) continues back to the » Access to medical care. The levels of diagnosis and
Answers
heart in the pulmonary vein. treatment of illness vary substantially. More of the
3 bronchus populations of African countries are without access
trachea to effective health infrastructures than in the other
bronchiole two regions, for example. Where there are fewer
alveoli doctors or care centres per head of the population
or in rural communities that are widely scattered,
the chances of diagnosis, treatment and preventative
10 Infectious diseases measures are minimal.
1 Present in the wall of the stomach are millions of » The cost of health provision. Some countries cannot
tiny pits called gastric glands. The cells in the gastric afford to buy medicines or vaccines, or only the
glands make and secrete the contents of the gastric relatively well-off can afford them. Few countries
juice. About 600 cm3 of gastric juice is secreted per have the equivalent of a health service so the poor
meal, secretion being co-ordinated with the presence do not get treatment.
of food. One of the components of gastric juice is 5 HIV/AIDs causes particular problems for the people
hydrochloric acid (strength 0.15M) at about pH 1. and the economies of less-developed countries such
This is sufficient to create an acid environment of as Zimbabwe or Zambia because it almost exclusively
pH 1.5–2.0 for the contents of the bolus, the optimum handicaps the young adult population at their time of
pH for the protein digesting enzymes of the gastric greatest economic activity and family building.
juice. The hydrochloric acid also kills many bacteria,
6 a) Exposure of pathogenic bacteria to sub-lethal doses
among other useful effects. of antibiotic may increase the chances of resistance
2 In cholera, chloride ions move from epithelium cells developing in that population of pathogens.
into the lumen of the gut by active transport caused by b) By varying the antibiotics used there is increased
protein pumps in the cell membrane, driven by ATP. likelihood of killing all the pathogens in a
Water moves by osmosis (a special case of diffusion), population, including any now resistant to the
in which metabolic energy is not involved. previous antibiotics used. This approach works
3 The insecticide DDT is harmless to humans at until multiple-resistance strains have evolved,
concentrations that are toxic to mosquitoes, but such as in strains of Clostridium difficile and
applied at these concentrations it rapidly collects Staphylococcus aureus, for example.
in body fat and is transferred from prey to predator 7 Antibiotics are added to the feed of intensively-reared
through the food chain, steadily increasing in livestock such as chickens and pigs. Here they reduce
concentration. It accumulates at the top of food or prevent the incidence of many diseases, and the
chains at concentrations that may cause harm. The animals are found to grow better with them. Possible
stability of the DDT molecule means that it only very dangers arise from the over-exposure of bacteria to
slowly biodegrades. This persistence is why it is so antibiotics – see Figure 10.27 (page 221).
effective, but is also why it is a health threat. By means
of her book Silent Spring, it was Rachael Carson who END OF TOPIC QUESTIONS
publicised this problem. These answers are for guidance only. They do not represent
4 These figures show us that, whatever the level of the full response required by questions in the examination.
TB infection in a region, about 10 per cent of those Cambridge Assessment International Education bears no
infected die from the condition.The proportion of responsibility for the example answers to questions taken
the population of Europe with TB is far lower than in from its past question papers which are contained in this
either of the other two regions. publication.
These differences in prevalence are most likely to be 1 a) From infected cattle (drinking unpasteurised milk
accounted for by three major factors: or eating their meat).
» Housing, which is related to a general level of b) It increases the chances of all the bacteria being
poverty and unemployment. Where the prevalence killed, as if the bacteria are resistant to one of
of TB is high the environmental and social the antibiotics, they may not be resistant to one
conditions (particularly housing) are likely to favour of the remaining three. If one of the antibiotics
transmission of the bacterium. Countries with causes such severe side effects that it has to be
high unemployment and low wages and countries stopped, there are still other antibiotics working.
experiencing local or civil wars are more likely It is unlikely that any mutation that may arise will
to have a major part of the population living in cause the bacteria to be resistant to more than one
crowded and unhealthy conditions. of the antibiotics.
500

c) The number of cases in TB has increased by 3 This is a self-assessment exercise – check your answer
Answers
approximately 25% over the time period, however, by referring to ‘HIV/AIDs’, pages 212–5.
the number of cases of MDR-TB has increased 4 This is a self-assessment exercise – check your answer
more than 200-fold, with a greater than ten times by referring to ‘Antibiotics’ (pages 216–21).
increase between 2005 and 2006, and another
more than doubling of reported cases between 11 Immunity
2011 and 2012. The total number of cases of TB
did not increase between 2011 and 2012. However, 1 See What recognition of ‘self’ entails, page 225 and
there was a reduction in the number of reported Figure 11.4, page 227.
cases of MDR-TB between 2013 (18 384) and 2014 2 Antigens may be present more or less anywhere in the
(17 386). body that can be contaminated from outside the body.
d) The increase in cases of TB indicates the conditions Antibodies exist in the blood and lymph and may be
for TB still are very prevalent for the population carried in the blood plasma anywhere that blood ‘leaks
(crowded and poorly ventilated accommodation). out’ to, including sites of invasions. They also occur
Because TB is easily transmitted, this means that on B-lymphocytes.
MDR-TB is also easily spread in the population. 3 See Figure 8.6, page 172.
The vaccination programme is not reaching a
4 Spleen cells and tumour cells cultured separately and
sufficient proportion of the population to provide
then mixed together. Mixture is cultured to produced
herd immunity. For the recent decrease in MDR-TB,
‘hybridoma’ cells. Resulting cells are separated and
this may be because people are more aware of the
tested for antibody required. Positive hybridoma
importance of finishing their course of antibiotics
cells are cultured further and produce antibody in
and are better educated about how TB is transmitted.
significant quantities.
However, there is still a huge proportion of MDR-TB
cases in the population, and the number of cases 5 a) The existence of memory cells avoid the steps to
of TB has also increased which suggests that less the production of activated T-lymphocytes. The
money is available to treat this disease. particular memory cell, once re-activated by the re-
invading antigen, switches to production of an excess
2 a) A e.g. cholera, see ‘Prevention of cholera’,
of the appropriate plasma cells and helper T-cells.
page 204
b) The initial response to an antigen by the immune
B e.g. malaria, see ‘Control measures’, page 206
system is slow. For sufficient antibodies to
C e.g. TB, see ‘How tuberculosis spreads’, page 208
overcome an infection takes weeks rather than
b) See Figure 10.8, page 206. On being introduced
days. When memory cells are present, many stages
into the bloodstream by a feeding mosquito,
of the initial response are omitted and antibodies
Plasmodium immediately enters liver cells. Here
are quickly assembled.
it is isolated from the patient’s immune system or
attack by macrophages, for example. In the liver 6 Immunity is the resistance to the onset of disease
cell the parasite reproduces asexually. When this after infection by harmful microorganisms or internal
stage of the parasite is released into the patient’s parasites. Long-lived specific immunity is a result of
blood it immediately enters red blood cells, and the action of the immune system and may be acquired
reproduction continues. The cycle of red blood cell naturally by previous infection, but can also be induced
invasion, reproduction and release (with toxins) is by vaccination. See Types of immunity, page 236.
then repeated. 7 Natural Artificial
c) A key part of the parasite’s lifecycle is completed in
Active antibodies received monoclonal
the mosquito vector. Only in the tropics and sub-
immunity via the placenta antibodies to treat
tropical regions are conditions favourable for the
tetanus
mosquito to survive long enough for reproduction
of the parasite within the vector. Passive measles infection polio vaccine
d) An epidemic is a disease that appears suddenly immunity
and then spreads rapidly in a specific area or
within a particular population group for a time, END OF TOPIC QUESTIONS
e.g. cases of food poisoning. A pandemic is an These answers are for guidance only. They do not represent
epidemic that spreads far more widely – typically the full response required by questions in the examination.
throughout a whole country, a whole continent, or Cambridge Assessment International Education bears no
the whole world, e.g. the influenza (flu) pandemic responsibility for the example answers to questions taken
in 1918. from its past question papers which are contained in this
publication.
501

1 a) The antibody has four polypeptide chains. antibodies to TAA are attached to drugs that kill
Answers
b) i) Each antibody consists of four polypeptide cells or inhibitors that block synthesis of key
chains held together by disulfide bridges tumour proteins. This helps the drugs to target
(–S–S–), forming a molecule in the shape of the cancer cells so they do not damage other,
a Y. The arrangement of amino acids in the healthy cells.
polypeptides that form the tips of the arms of 3 a) red bone marrow
the Ys, the two variable regions of the antibody, b) i) A is a macrophage. B is a B-lymphocyte. C is a
are unique to that antibody. It is these regions T-lymphocyte.
that hold the highly specific binding site for a ii) D is the thymus gland.
particular antigen. c Lymphocytes detect matter entering from outside
ii) The constant region binds to the cell surface our bodies (including foreign macromolecules
receptors on B-lymphocytes. and microorganisms) as different from ‘self’
c) i) The immune system of a mouse is stimulated to (body cells and our own proteins). Non-self
produce antibodies by injection of an antigen. invading macromolecules and microorganisms
The mouse spleen cells are then cultured by are known as antigens. On the arrival of a specific
tissue culture; mouse tumour cells are removed antigen, B-lymphocytes with surface receptors
and cultured. Both types of cell are mixed and (antibodies) bind to it. The antigen is then taken
cultured. Some B-lymphocyte cells fuse with into the cytoplasm by endocytosis before being
tumour cells to produce a hybrid cell called a expressed on the cell surface membrane of the
hybridoma. These hybridomas are detected and B-lymphocyte. T-lymphocytes respond to antigens
isolated. These cells, once isolated, are cultured when presented on the surface of other cells.
and screened for a particular monoclonal Macrophages engulf antigens they encounter.
antibody. Production is then scaled up in a When T-lymphocytes come into contact with the
fermenter. macrophages they are activated and bind to the
ii) Monoclonal antibodies only detect one B-lymphocytes, activating the B-lymphocytes
antigen; they are therefore specific and can which divide rapidly by mitosis, forming a clone of
distinguish between strains of pathogen. They cells called plasma cells. The plasma cells produce
can detect the location of tissues expressing and export large quantities of antibodies, which
the antigen or the location of the cancer cells, overcome the antigens.
since they can be tagged, for example with a
fluorescent label.
Monoclonal antibodies can be produced that 12 Energy and respiration
specifically target and kill the cancer cells. 1
Many drugs and treatments effective against Pi Pi Pi
cancer are also harmful to other, healthy
cells. The specificity of antibodies avoids this
problem.
2 a) A monoclonal antibody is a single antibody that is 2 The important features of ATP are that it is:
stable and can be used over a period of time. Each » a substance that moves easily within cells and
specific antibody is made by one particular type organisms – by facilitated diffusion
of B-lymphocyte. The lymphocyte is fused with a
» formed in cellular respiration and takes part in
cancer cell which goes on dividing indefinitely, so
many reactions of metabolism
it continues to secrete the antibodies in significant
quantities. (See Figure 11.12, page 233.) » able to transfer energy in relatively small amounts,
b) Monoclonal antibodies are used in pregnancy sufficient to drive individual reactions.
testing. Pregnant women have a significant 3 See Extension: The respiration of fats and proteins,
concentration of the hormone human chorionic page 245, and Excretion, blood water balance and
gonadotrophin (HCG) in their urine. Monoclonal metabolic waste, particularly Figure 14.11, page 301.
antibodies to HCG have been engineered to also 4 C15H31COOH = C16H32O2
carry coloured granules which provide a visual C16H32O2 + 2302 → 16CO2 + 16H20 + Energy
confirmation of pregnancy. Monoclonal antibodies
CO2 produced
are used in the treatment of cancer. Cancer cells RQ =
carry specific tumour-associated antigens (TAA) O2 taken in
on their cell surface membrane. Monoclonal RQ = 16 ÷ 23 = 0.696
502

5 a) 1.2 c) See Extension: Respiration as a series of redox
Answers
reactions, page 243.
seedling B
1 9 a) Glycogen
b) Starch
0.8 10 Endergonic reactions require energy input, because
the products have more potential energy than
the reactants – see Figure 3.1, page 62. Note: the
RQ
0.6
alternative type of reaction is one in which the
products have less potential energy than the reactants.
0.4
seedling A These reactions transfer energy as heat and work and
are called exergonic reactions.
0.2
11 Glycolysis (the conversion of glucose to pyruvate)
which occurs in the cytosol (the aqueous part of
0 the cytoplasm that surrounds organelles such as
0 2 4 6 8 10 12
the mitochondria) does not require oxygen for
time after germination/days
completion.
b) Seedling A has a pattern of RQ change in early
12 Use of a single water bath at a favourable temperature –
germination typical of seeds with a food store
perhaps 25°C; repetition of the experiment with a
consisting mainly of carbohydrate. (Actually, this
range of dilute glucose solutions (the substrate).
data is from germinating wheat fruits which contain
70% carbohydrate, 2% lipid (oil) and 12% protein). 13 Lactate and a small amount of ATP are the final
Seedling B has a pattern of RQ change in early products of anaerobic respiration in muscle fibres.
germination typical of seeds with a food store 14 In the absence of oxygen reduced NAD accumulates
consisting mainly of lipid. (Actually, this data is and oxidised NAD reserves are used up. In the absence
from germinating flax seeds which contain 2% of oxidised NAD, pyruvate production by glycolysis
carbohydrate, 55% lipid (oil) and 20% protein). slows and stops, so subsequent steps in respiration
6 The following are produced during glycolysis: reduced must stop too.
NAD (c), ATP (e) and pyruvate (g). 15 Presence of aerenchyma tissue of stem, leaf and root;
7 a) In respiration, all the hydrogen atoms are gradually ability of roots to respire anaerobically – with relatively
removed from glucose, catalysed by dehydrogenase high tolerance of ethanol.
enzymes. The hydrogen atoms are added to 16 In the respirometer, the far side of the U-tube
hydrogen acceptors, usually NAD (nicotinamide manometer is the control tube (A). Here, conditions
adenine dinucleotide, page 244), forming reduced are identical to those in the respirometer tube, but in
NAD. NAD is a coenzyme that works with specific the former, no living material is present. However, any
dehydrogenase enzymes in the oxidation of change in external temperature or pressure is equally
substrate molecules by the removal of hydrogen. experienced by both tubes, and their effects on the
b) Decarboxylation is the removal of carbon from level of manometric fluid are equal and opposite, and
organic compounds by the formation of carbon they cancel out.
dioxide. For example, glucose consists of six
carbon atoms. All six carbon atoms are removed END OF TOPIC QUESTIONS
at different stages of respiration, one at a time, These answers are for guidance only. They do not represent
and given off as carbon dioxide. A specific the full response required by questions in the examination.
decarboxylase enzyme is involved in each case. Cambridge Assessment International Education bears no
The first decarboxylation in aerobic respiration responsibility for the example answers to questions taken from
occurs in the reaction linking glycolysis with its past question papers which are contained in this publication.
the Krebs cycle, when pyruvate is converted to a 1 a)
two-carbon molecule. The other decarboxylation Contents of dishes ATP produced
reactions of aerobic respiration occur in steps in mitochondria + ADP + Pi + acetyl CoA
the Krebs cycle. + oxygen ✓
8 a) A substrate is a molecule that is the starting point mitochondria + ADP + Pi + acetyl CoA ✗
for a biochemical reaction; it forms a complex with
mitochondria + ADP + Pi + low ✗
a specific enzyme. An intermediate is a molecule concentration of protons (H+)
formed as a component of a metabolic pathway.
b) See Glycolysis, page 250, and The link reaction mitochondria + ADP + Pi + high
concentration of protons (H+) ✓
and the Krebs cycle, pages 251–2.
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b) Water will enter the mitochondrion by osmosis
13 Photosynthesis
Answers
and the mitochondrion will swell and may burst.

c) Oxygen is the final electron acceptor in the 1 Adapt part of the diagram of the chloroplast
electron transport chain. (diagrammatic view) in Figure 13.1. Select your
d) ATP synthase annotations from Table 13.1 (page 270).
e) Surface area of mitochondrion greatly increased by 2 See What happens in photosynthesis and Figure 13.7
intucking to form cristae. The electron transport (page 275).
chain and ATP synthase enzymes are housed here, 3 The starting materials (carbon dioxide and water) are
so the opportunities for ATP synthesis are enhanced. in an oxidised (low energy) state. The end product
The cristae are impermeable to hydrogen ions of photosynthesis – glucose, is in a reduced (higher
(protons) – allowing the formation of a potential energy) state.
difference between the intermembrane space and
4 See Figure 3.1, page 62.
the matrix, making phosphorylation possible.
5 Chlorophyll is a mixture of pigments that absorbs
2 a) many of the component wavelengths of white light
Component except green, which it transmits or reflects (hence the
of process Location of the green colour of chlorophyll).
of aerobic process in the 6 Knowing the Rf value of a metabolite or pigment
respiration eukaryotic cell Chief products helps in the identification of that substance when the
Glycolysis Cytoplasm Pyruvate, small composition of a different mixture is investigated.
amount of ATP However, Rf values depend upon the same composition
and reduced NAD and concentration of solvent being used and also the
same type and grade of chromatography paper.
Link reaction Ccytoplasm Acetyl coenzyme
A 7 The hydrophobic ‘tail’ of the chlorophyll molecule is
unable to form hydrogen bonds with water molecules,
Kreb’s cycle Matrix of the Carbon dioxide, making chlorophyll insoluble in water.
mitochondria reduced NAD (and
reduced FAD) 8 Chromatography allows the complete separation of
components of mixtures. It is an ideal technique for
Oxidative Membrane of the ATP, water separating biologically active molecules obtained from
phosphorylation mitochondria samples of tissue since biochemists are often able to
(cristae) isolate only very small samples.
b) i) Decarboxylation is a chemical reaction that 9 Reduced NADP and ATP are the products of the
removes a carboxyl group from a compound light-dependent stage of photosynthesis required (and
and releases carbon dioxide. promptly used) in the light-independent stage. The
ii) Dehydrogenation is a chemical reaction that light-independent stage occurs in the stroma, so the
removes hydrogen from a compound. formation of reduced NADP and ATP on the side of
thylakoid membranes that face the stroma makes them
3 a Enters the mitochondria: oxygen, pyruvate, fatty
instantly available.
acids, ATP, phosphate
10 There are three ways in which the gradient in protons
Leaves the mitochondria: water, carbon dioxide, ATP
between the thylakoid space and the stroma is generated:
b i) 102 ÷ 145 = 0.70
ii) Generally respire aerobically, but a mix of » the splitting of water on the thylakoid membrane on
different substrates (carbohydrates, lipids and the thylakoid space side is a source of hydrogen ions
proteins) have different RQ values. there
4 This is a self-assessment exercise – check your answer » the energy made available as excited electrons from
by referring to the following sections: photosystem II are passed along the electron carrier
a) ‘The electron transport chain and oxidative chain to photosystem I is used to pump hydrogen
phosphorylation’ (page 252) ions from the stroma to the thylakoid space
b) ‘Anaerobic respiration is less efficient than aerobic » the formation of reduced NADP on the stroma side
respiration’ (page 260) of the thylakoid membrane removes hydrogen ions
c) ‘The pathways of anaerobic respiration’ (page 259) there (reducing their concentration in the stroma).
5 a) i) cytoplasm 11 a) The ultimate fate of electrons displaced from the
ii) phosphorylation 1 and 3; oxidation 5; reaction reaction centre of photosystem I in non-cyclic
in step 5–substrate-linked phosphorylation photophosphorylation is to be retained in reduced
b) These cancer cells need more glucose and use little NADP.
oxygen, as they only obtain a small amount of ATP b) The ultimate fate of electrons displaced from
per glucose molecule by glycolysis. the reaction centre of photosystem I in cyclic
504

photophosphorylation is to be returned to the temperature. At high light intensity, temperature is
Answers
place in photosystem I from which they came. the limiting factor for the photosynthetic reactions.
12 In this demonstration of the Hill reaction, the isolated The increased temperature causes the molecules
chloroplasts are provided with an electron acceptor involved to have increased kinetic energy, leading to
dye (DCPIP). The chlorophyll at the reaction centre is higher probability of enzyme-substrate complexes
oxidised by light energy and in this state is able to split being formed, and so increasing the rate of reaction.
water by removing electrons. So DCPIP is the electron At low light intensities, light is the limiting factor.
acceptor in this demonstration of the Hill reaction and b) i) The absorption spectrum shows the absorption
the electrons come from water. of different wavelengths of light by different
chloroplast pigments. The action spectrum
13 Autotrophic nutrition of plants supports not only the
shows the rate of photosynthesis at different
plant, but also (indirectly) the primary consumers that
wavelengths of light.
feed on it and any higher-level consumers that are in
ii) The light absorbed by the chloroplast pigments
the same food chain or web. Consequently, the carbon
is used in photosynthesis. There is the highest
atoms making up almost all living things have been in
rate of photosynthesis at the wavelengths that
a carbon dioxide molecule that has been catalysed by
are absorbed best (at wavelengths 430 nm and
rubisco at some stage.
670 nm).
14 A thermometer is required in the glass tube with the c) It forms part of a light harvesting cluster of
pond weed (in a position that does not interfere with pigments that may absorb light wavelengths that
the supply of light to the plant), so that the temperature chlorophyll a does not, and passes the energy on
at which photosynthesis is measured is known. Also, it to chlorophyll a.
is advisable to check that the pond weed sample is not
2 a) See Figure 13.1, page 269.
subjected to an unplanned rise in temperature as the
b) These annotations should be added to the diagram:
intensity of light is increased, for example.
Grana – site of the light-dependent reactions of
15 a) The biochemical steps of photosynthesis are photosynthesis; the thylakoid membrane provides
dependent on the action and activity of numerous a large surface area in which ATP synthase and the
enzymes. As these are made of protein, they are pigment molecules of the photosystems occur.
progressively denatured and rendered inactive at Stroma – site of the light-independent reactions of
high temperatures. photosynthesis; it contains large quantities of the
b) As water evaporates from the surfaces of mesophyll enzyme rubisco which fixes carbon dioxide.
cells during transpiration, cooling occurs. Double membrane – allows carbon dioxide to enter,
16 a) Prevention of autolysis of cell organelles oxygen to leave and the products of photosynthesis
(particularly the chloroplasts) as hydrolytic to be translocated to the rest of the plant.
enzymes, held in previously intact lysosomes, are Starch grains – sugars may be converted into
released into the homogenised cytoplasm. starch for temporary storage.
b) Room temperature was selected as the working c) Single-celled algae are easier to culture than whole
temperature at which the Hill reaction was plants; they can be used directly in experiments
investigated at. without the need for preparation; they are not
c) To maintain a constant pH favourable for the necessarily destroyed during an experiment. If
enzymes of the chloroplast. the experiment is using chlorophyll, this needs to
d) Tube 1 – colour change from blue to colourless be extracted from the whole plant. In doing this,
Tube 2 – colour remains blue it is separated from the membrane systems of the
e) Tube 3 – confirms that chloroplasts are required chloroplasts so, although it can still absorb light, it
for the Hill reaction. cannot use it to make sugar. Single-celled algae can
Tube 4 – confirms the role of DCPIP as the be used directly and so the rate of photosynthesis
hydrogen acceptor. can also be measured in experiments. A culture
of Chlorella, a unicellular alga, was used in these
END OF TOPIC QUESTIONS experiments, in place of mesophyll cells. This
These answers are for guidance only. They do not represent was because they have similar photosynthetic
the full response required by questions in the examination. processes and they allow easy sampling.
Cambridge Assessment International Education bears no 3 a) The light-dependent stage of photosynthesis
responsibility for the example answers to questions taken from involves photochemical reactions. Water is split
its past question papers which are contained in this publication. by light energy (photolysis) and reducing power
is generated in the form of reduced NADP. Energy
1 a) At high light intensities, the rate of photosynthesis
transfer occurs when ATP is formed from ADP and
increases linearly with the temperature (up to
phosphate in the process of photophosphorylation.
20°C). At low light intensities, there is very
Oxygen is released as a waste product. The
little increase in the rate of photosynthesis with
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light-dependent stage of photosynthesis takes ribulose bisphosphate (RuBP), in the presence
Answers
place in the grana of the chloroplast. Chlorophyll of ribulose bisphosphate carboxylase (rubisco).
molecules are arranged in structures called RuBP is a five-carbon sugar. When carbon dioxide
photosystems and these are held in the thylakoid is added to it, it forms two molecules of the
membranes of the grana. three-carbon compound glycerate-3-phosphate
The chlorophyll and accessory pigments harvest (GP). In the second step, GP is reduced to triose
light energy and funnel the energy to the single phosphate, a three-carbon sugar. This reaction
chlorophyll a molecule called the reaction centre. In requires reduced NADP and ATP, both products
photosystem I the reaction centre is activated by light of the light-dependent stage of photosynthesis.
of wavelength 700 nm. In photosystem II the reaction In the final step, the acceptor molecule (RuBP)
centre is activated by light of wavelength 680 nm. is regenerated. For every six molecules of triose
In non-cyclic phosphorylation, the light energy phosphate formed, five are used to form three
reaching PSII activates a pair of electrons in the molecules of RuBP. Energy from ATP is required.
chlorophyll molecule of the reaction centre and From the other molecule of triose phosphate,
these are raised to an excited state. They are other compounds are synthesised. These include
captured by an electron acceptor in the nearby carbohydrates, lipids and amino acids. These
chain of electron carriers (proteins held in the conversions also require energy from ATP.
thylakoid membrane). The loss of the electrons 4 a) Rubisco is the enzyme ribulose bisphosphate
from the chlorophyll molecule causes it to be carboxylase which occurs in green plant leaves.
oxidised which, in turn, causes it to acquire It catalyses the fixation of carbon dioxide in the
electrons from water. In this process water is split, light-independent stage of photosynthesis. Rubisco
giving off oxygen as a waste product and hydrogen is the most abundant protein since green plants
ions. As the excited electrons from PSII are passed make up a large part of the biomass of the planet.
along the chain of electron carriers, their energy b) Competitive inhibitors are molecules that resemble
level falls back to the ground state. The energy the substrate in shape. They therefore compete with
transferred from them causes the pumping of the substrate to occupy the active site. Rubisco is
hydrogen ions from the stroma of the chloroplast competitively inhibited by oxygen in chloroplasts.
into the thylakoid spaces where they accumulate, c) For photosynthesis to yield useful products,
creating a proton gradient. carbon dioxide needs to combine with ribulose
At the same time, light also raises electrons of PSI bisphosphate, but in 25% of the reactions of
to an excited state. These are also captured by photorespiration oxygen combines with RuBP.
electron acceptors in electron carrier molecules. While photorespiration does eventually result in
The chlorophyll molecules in PSI are oxidised glycerate 3-phosphate, there is a net loss of carbon
but instead of acquiring electrons from water, and nitrogen and it uses up ATP.
they acquire electrons from PSII. As the excited 5 a) i) glycolysis, Kreb’s cycle, link reaction
electrons from PSI are passed along the chain of ii) Role of the carriers in the inner membrane is to
electron carriers, their energy level falls back to the split hydrogen into H+ and electrons. Energy
ground state. The energy transferred from them is used to pump the hydrogen ions into the
causes a molecule of reduced NADP to be formed intermembrane space.
from NADP and hydrogen ions in the stroma. iii) Y oxygen; Z ATP synthase
Finally, photophosphorylation occurs and ATP is b) The folds increase the surface area available for
synthesised. In this, the hydrogen ions that have ATP synthase and so more ATP can be produced.
accumulated in the thylakoid space diffuse down the 6 This is a self-assessment exercise – check your answer
concentration gradient back into the stroma through by referring to the sections headed ‘Light as an energy
the pore in the ATP synthase enzyme molecules source’ (page 271) and ‘The absorption and action
held in the thylakoid membranes. This causes the spectra of chlorophyll’ (page 274) and your own
synthesis of ATP from ADP and phosphate ions. laboratory practical work record, or by discussions
b) The Calvin cycle is driven by the products of the with peers and your teacher or tutor.
light-dependent stage of photosynthesis. It is light
independent, although the enzyme it involves,
rubisco, is light activated, and takes place in the 14 Homeostasis
stroma of the chloroplasts. During the process, 1 a) Carbon dioxide is an acidic gas which, if it were
carbon dioxide is fixed by ribulose bisphosphate to accumulate in the blood, would alter the pH of
and ultimately converted into all the organic the plasma solution. The normal pH of the blood is
molecules needed for life. 7.4. For life to be maintained it must remain within
In the first step of the Calvin cycle, carbon the range pH 7.0–7.8. This is largely because blood
dioxide is combined with an acceptor molecule, pH affects the balance of essential ions which are
506

transported in the plasma solution. Efficient removal 7 a) A negative feedback system consists of a receptor, a
Answers
of respiratory carbon dioxide from the lungs is as coordinator and an effector. In osmoregulation we
important to life as efficient uptake of oxygen. have:
b) Receptor: chemoreceptors in the medulla, carotid Receptor: osmoreceptors in the hypothalamus
artery and aorta Coordinator: hypothalamus and posterior pituitary
Co-ordinator: inspiratory and expiratory centres of gland from where ADH is released
the respiratory centre in the medulla Effector: collecting ducts of the nephrons in the
Effectors: muscles of the ribs and the diaphragm medulla of the kidneys.
that bring about ventilation of the thorax. b) The osmoreceptors in the hypothalamus, together
2 The following organelles would be directly involved in with the receptors in the aorta and carotid arteries
hormone production and discharge: detect the change in the water content of the blood.
Nerve impulses from the receptors are transmitted
» the nucleus – the site of the gene for the hormone
to the hypothalamus and pituitary gland.
(a protein) concerned, together with the enzyme
machinery for the production of relevant messenger 8 See Figure 4.17 and Figure 4.18 (pages 95 and 96).
RNA 9 Stomata open and close in response to changes in
» pores in the nuclear envelope – exit points for the turgor in the guard cells. See The opening and closing
messenger RNA on its way to the cytosol of stomata, pages 313–14 and Abscisic acid and water
stress in the leaf page 314.
» ribosomes attached to the endoplasmic reticulum
(RER) – the site of the formation of the hormone
» vesicles cut off from the RER – transport of the
hormone across the cytosol to the cell surface These answers are for guidance only. They do not represent
membrane the full response required by questions in the examination.
» the cell surface membrane – to which the vesicles responsibility for the example answers to questions taken from
containing the hormone fuse allowing discharge of its past question papers which are contained in this publication.
the hormone.
3 When a diabetic patient assesses their blood glucose 1 a) Maintaining a constant and stable internal
by means of a biosensor, the measurement is of the environment in the body.
amount of glucose present at the moment the reading b) i) A pelvis; B ureter
is taken. When readings are taken of glucose levels ii) U leader line to cortex; L leader line to medulla;
in the urine, there has been an inevitable lag time C leader line to renal vein
before blood glucose level is reflected in the urine. c) Antidiuretic hormone (ADH) is produced in
Colorimetric readings involve a level of subjective the hypothalamus and stored in vesicles at the
judgment that the biosensor avoids, too. ends of neurosecretory cells in the posterior
pituitary gland. When nerve impulses from the
4 a) The force that drives ultrafiltration in the glomerulus
hypothalamus trigger the release of ADH into the
is the blood pressure generated by the muscles
capillary networks in the posterior pituitary, ADH
of the ventricles. This pressure is heightened by
circulates in the bloodstream. When the water
the efferent arteriole of the glomerulus being of a
content of the blood is low, antidiuretic hormone
smaller diameter than the afferent arteriole.
(ADH) is secreted from the posterior pituitary
b) Water, useful ions, glucose and amino acids, along
gland. When the water content of the blood is high,
with urea.
little or no ADH is secreted. ADH changes the
5 a) Brush border is made up of microvilli. Microvilli permeability of the walls of the collecting ducts.
provide a vastly increased surface area of cell
surface membrane in contact with the filtrate. In The cell surface membranes of the cells that form
the membrane there are protein pumps which the walls of the collecting ducts contain a high
actively and selectively absorb useful metabolites. proportion of channel proteins called aquaporins
b) See Facilitated diffusion, page 90, and that are capable of forming an open pore running
Figure 14.16, page 305. down their centre. Aquaporins are selectively
permeable to water molecules and therefore increase
6 In a counter-current flow system fluids flow in the rate of water diffusion (osmosis) through the
opposite directions in parallel and adjacent tubes. So membrane. This is because the water molecules
the limbs of the loop of Henle and the vasa recta as no longer have to pass through the lipoprotein
it occurs besides the loop of Henle are both counter- membrane structure that restricts their flow. In this
current systems. Exchange occurs between these
way the presence of ADH ensures that a maximum
systems and a gradient is maintained along the entire
volume of water can be reabsorbed into the medulla
exchange surface.
of the kidney and back into the bloodstream.
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When ADH is present in the blood circulating c) Abscisic acid, a growth inhibitor in plants, is
Answers
past the kidney tubules, this hormone causes produced in the chloroplasts under conditions
the protein channels present in the collecting of water shortage (it is a ‘stress hormone’). On
duct cell surface membranes to be open. As a reaching the guard cell, it initiates stomatal closure
result, water diffuses out into the medulla and by triggering release of chloride ions (in a role as
very little diffuses from the medulla into the second messengers), and this leads to reversal of
collecting ducts. the opening mechanism.
2 This is a self-assessment exercise – check your answer 4 This is a self-assessment question – check your
by referring to the section Homeostasis in action – answer by reference to:
control of blood glucose concentration (pages 294–8). a) ‘Homeostasis in action – control of blood glucose
concentration’ (pages 294–8).
3 a) Stomata are tiny pores of the epidermis of leaves
b) ‘The three-stage process of cell-signalling’ (page 298).
through which gas exchange can occur; most
occur in the epidermis of leaves, but some occur
in stems; in a typical broadleaf, stomata are 15 Control and coordination
concentrated in the lower epidermis; each stoma
consists of two elongated guard cells attached to 1 The effects of hormones are restricted to cells with
ordinary epidermal cells that surround them and specific receptors on the cell surface membrane to
securely joined together at each end; the guard which they attach or with which they react, so they
cells are detached and free to separate along the affect only the target cells or tissues.
length of their abutting sides – when they separate,
2
a pore appears between them. Motor Intermediate
Answers should include labelled drawings of two neurone Sensory neurone neurone
guard cells in situ, sectioned to show cross-section Receives Receives impulses Receives
(variable wall thickness), the pore, and their impulses via many impulses via
relationship with the surrounding epidermal cells via many (typically long) many (typically
(see Figure 14.20, page 312) dendrites dendrons, each short) nerve
b) Stomata open and close due to changes in turgor protected by a fibres, which are
pressure of the guard cells; opening occurs when myelin sheath not myelinated
water is absorbed by the guard cells from the Passes impulse Passes impulse Passes impulse to
surrounding epidermal cells – the guard cells to a muscle to dendrites of dendrites or the
then become fully turgid, and each push into fibre or gland a intermediate cell body of motor
the epidermal cell beside them; this direction of via a single neurone or its cell neurones via
movement occurs because of the way cellulose axon, which is body via a single many short nerve
is laid down in the walls; turgor rises due to the protected by a axon, which is fibres, which are
following: myelin sheath protected by a not myelinated
• Potassium ions (K+, a cation) are pumped myelin sheath
into the guard cell vacuole, from surrounding 3
cells, by proteins of the plasma membranes, Location of
Stimulus detected Receptor receptor
triggered by light (blue light wavelengths).
Calcium ions play a part in this process. Mechanoreceptors
• Starch, stored in the guard cells, is converted Movement and Stretch Skeletal muscle
to organic acids, particularly malate. These position receptors,
anions accompany the K+ cations in the e.g. muscle
guard cell vacuole. The accumulation of these spindles,
substances in the guard cell vacuole causes the proprioceptors
water potential there to become more negative. Blood pressure Baroreceptors Aorta and
So, net uptake of water from the surrounding carotid artery
ordinary epidermal cells occurs, making the
Thermoreceptors
guard cells turgid. Reversal of these changes
causes water loss – the guard cells become Internal Cells of the Brain
flaccid and the pore closes again. temperature hypothalamus
A labelled drawing of these changes occurring in Chemoreceptors
two guard cells in situ, in light and darkness, as Blood O2, CO2, H+ Carotid body Carotid artery
shown in Figure 14.24, page 314. Osmotic Osmoregulatory Brain
concentration of centre in the
the blood hypothalamus
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4 In positive feedback the effect of a deviation from ii) Stimulus A was below the threshold needed to
Answers
the normal or set condition is to create a tendency to generate a potential.
reinforce the deviation. Positive feedback intensifies iii) The refractory period limits the frequency of
the corrective action taken by a control system, action potentials sent. Action potentials travel
leading to a ‘vicious circle’ situation. Imagine a car in in one direction
which the driver’s seat was set on rollers (rather than iv) During an action potential, locally the
being secured to the floor) being driven at speed. The sodium channels open, Na+ rushes in and
slightest application of the foot brake causes the driver the membrane depolarises. The presence of a
to slide and to press harder on the brake as the car myelin sheath affects the speed of transmission
starts to slow with an extreme outcome. of the action potential because the membrane
Biological examples of positive feedback are rare, is prevented from depolarising by the electrical
but one can be identified at the synapse. When a resistance of the myelin sheath. Thus action
wave of depolarisation (a nerve impulse) takes effect potentials can only occur at junctions in the
in the postsynaptic membrane, the entry of sodium sheath, known as the nodes of Ranvier, that
ions triggers the entry of further sodium ions at a occur at 1–2 mm intervals. Consequently, the
greater rate. This is a case of positive feedback. The action potentials are forced to jump from node
depolarised state is established and the impulse moves to node (salutatory conduction). This is an
along the postsynaptic membrane. advantage, as it greatly speeds up the rate of
transmission.
In negative feedback the effect of a deviation from
the normal or set condition is to create a tendency to 2 a) The endocrine system consists of endocrine
eliminate the deviation. Negative feedback is a part of glands which secrete chemical messengers called
almost all control systems in living things. The effect of hormones. Hormones are carried indiscriminately
negative feedback is to reduce further corrective action of in the bloodstream but only act at specific sites
the control system once the set-point value is reached. called target organs.
5 a) See The resting potential, page 323. Hormones typically cause changes to specific
b) See The action potential, page 324. metabolic reactions in their target organs. They
only remain in the bloodstream for a brief period
6 See The refractory period, page 325.
before being broken down in the liver. Examples
7 See Speed of conduction of the action potential, include insulin, which regulates blood glucose,
page 326. and adrenaline, which controls the body’s ‘flight
8 a) Transmitter substances are produced in the Golgi or fight’ response.
apparatus in the synaptic knob and held in tiny The nervous system consists of nerve cells
vesicles prior to use. called neurones and the central nervous system
b) See Figure 15.11, page 328. (the brain and spinal cord). Neurones transmit
9 See The ultrastructure of skeletal muscle, and impulses which are momentary reversals of
Figures 15.12, 15.13, and 15.14, pages 329–31. electrical potential and can travel at speeds of
10 Growth consists of a permanent, irreversible increase between 30 and 120 metres per second. The
in size; development is a change in shape, form and impulses are targeted at specific organs.
complexity of an organism. b) Auxins are plant growth regulators which are
manufactured by cells undergoing repeated cell
END OF TOPIC QUESTIONS division, such as those found in stem and root tips.
These answers are for guidance only. They do not represent Apical dominance occurs when a plants grows
the full response required by questions in the examination. upwards rather than producing lateral buds. This
Cambridge Assessment International Education bears no happens because the auxin indoleacetic acid (IAA),
responsibility for the example answers to questions taken from which is produced in the apical bud at the tip of
its past question papers which are contained in this publication. the stem, is carried down the stem in the xylem
and prevents the growth of lateral buds. Auxins
1 a) Sensory receptor cells detect stimuli, such as interact with other plant growth substances to
pressure, light, heat, vibrations from sound and control growth.
chemicals, and convert the stimuli into electrical
3 a) i) A, aleurone layer; B, endosperm; C, embryo
energy so that an action potential is generated and
ii) The embryo produces gibberellin that moves
the nerve impulse travels along a sensory neuron
into the aleurone layer (arrow 1). Gibberellin
to the spinal chord or the brain.
stimulates production of amylase. Amylase
b) i) pump operating, C or D and E; Na+ channels
moves into the endosperm (arrow 2) where it
open, C; K+ channels open, D
breaks down starch to maltose. The maltose
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moves into the embryo (arrow 3) where it meiosis I and meiosis II, the chromosome number is
Answers
provides energy for production of ATP for halved in the four cells produced following meiotic
germination of the wheat. cell division.
4 a) See Figure 15.10, page 327. 3 a) Metaphase I and II
b) 1 The arrival of an action potential at the b) Mid prophase I
synaptic knob opens calcium channels in the c) Late prophase I
presynaptic membrane and calcium ions flow d) Anaphase II
in from the synaptic cleft. e) Anaphase I
2 The calcium ions cause vesicles of transmitter f) Telophase II
substances, such as acetylcholine (ACh) or 4
noradrenaline, to fuse with the presynaptic Mitosis – a Meiosis – a
membrane and release the transmitter replicative reductive
substances into the synaptic cleft. division division
3 The transmitter substance diffuses across Consequences All cells » Ensures
the synaptic cleft and binds with receptor carry the maintenance of
proteins. In the postsynaptic membrane same genetic the chromosome
there are specific receptor sites which act as information as number in
channels to allow specific ions, such as Na+ the existing body cells from
or Cl−, to pass. As sodium ions rush into the cells from generation to
cytoplasm, depolarisation of the postsynaptic which they are generation
membrane occurs. As more ACh molecules formed, and » Is a source
bind, depolarisation reaches the threshold which they of variation
level and an action potential is generated in the share with (important for
postsynaptic neurone. surrounding the survival of
c) Synapses are the link between neurones. They cells the species in a
ensure that impulses only flow in one direction. changing world)
They allow neurones to integrate with several post- Product Two identical Four, non-identical
synaptic neurones. They prevent neurones being cells, each with cells, each with the
stimulated by low-level impulses and they prevent the diploid haploid number of
effectors being over stimulated. number of chromosomes
chromosomes
16 Inheritance Significance » Permits Contributes to

growth and genetic variability by:
1 a) See Diploid organisms contain homolgous pairs of repair within » reducing the
chromosomes, page 343. multicellular chromosome
b) Mitosis and meiosis are divisions of the nucleus organisms number by half,
by very precise processes; they ensure the correct » Also, for permitting
distribution of chromosomes between the asexual subsequent
daughter cells. reproduction fertilisation and
The daughter cells produced by mitosis have a set the combination of
of chromosomes identical to each other and to the the genes of two
parent cell from which they were formed. In growth parents
and development it is essential that all cells carry » permitting the
the same information as the existing cells. Similarly random assortment
when repair of damaged or worn out cells occurs, of maternal
the new cells are exact copies of what they replace. and paternal
chromosomes
Meiosis occurs in the life cycle of all organisms
» allowing
that reproduce sexually. In meiosis four daughter
recombination
cells are produced, each with one member of
of segments of
each homologous pair of the chromosomes of the individual maternal
parent cell, known as the haploid (n) state. Halving and paternal
of the chromosome number is essential since at homologous
fertilisation the number is doubled. chromosomes
2 A major event of interphase is the replication of the during crossing
chromosomes. By the omission of this stage between over
510

5 The idea that the characteristics of parents were From the genetic diagram, the offspring (F2) to be

Answers
blended in their offspring was disproved by expected and the proportions are:
investigating the progeny of crosses of organisms Genotype CR CR CR CW CW CW
with contrasting characteristics (such as ‘tall’ and
‘dwarf’ pea plants) through a second and sometimes Ratio 1 2 1
subsequent generations. Large samples were used and Phenotype red roan white
the experiments were repeated, confirming that the 8 » Mr and Mrs Jones are blood groups A and B, which
observed ratios were statistically significant. might produce any one of:
6 We can expect a ratio of 3 : 1 among the progeny only AA × BB → blood group AB
if three conditions are met:
AO × BO → blood groups A, B, AB or O
» fertilisation is random – each fertilisation is
independent of all the others AA × BO → blood groups AB or A
» there are equal opportunities for survival among the AO × BB → blood groups AB or B
offspring So Mr and Mrs Jones could be the parents of any of
» large numbers of offspring are produced. the four children.
In breeding experiments with plants such as the » Mr and Mrs Lee are blood groups B and O, which
pea plant, exact ratios may not be obtained because might produce either of:
of parasite damage, due to the action of browsing BB × OO → blood group B
predators on the anthers or ovaries in some flowers BO × OO → blood group B or O
or because some pollen types fail to be transported by So Mr and Mrs Lee might be the parents of either the
pollinating insects as successfully as others. blood group B or the blood group O child.
7 The layout of your monohybrid cross will be as in » Mr and Mrs Gerber are both blood group O, which
Figure 16.13 (page 355), but the parental generation can produce only:
(P) will have genotypes (if you have chosen C to
OO × OO → blood group O
represent the gene for coat colour):
CR CR × CW CW So Mr and Mrs Gerber must be the parents of the
blood group O child.
where CR represents the allele for red coat and CW

represents the allele for white coat. The gametes the » This also means that, by elimination, Mr and Mrs
parental generation produce will be: Lee must be the parents of the blood group B child.
CR and CW » Mr and Mrs Santiago are blood groups AB and O,
The offspring (F1) will have the genotype CR CW
which might produce:
and the phenotype will be ‘roan’.
AB × OO → blood groups A or B

In a sibling cross of the F2 generation the gametes of Since Mr and Mrs Lee are the parents of the blood
both siblings will be: group B, Mr and Mrs Gerber must be the parents of
1
2
CR and 1
2
CW the blood group A child.
» By elimination, Mr and Mrs Jones must be the
CR CW
parents of the blood group AB child.
CR CR CR CR CW
9 a) See Red–green colour blindness, page 359.
CW CR CW CW CW b) See Sex linkage, page 358, and Figure 16.16, page
359.
R
s
1/2
te
ga
/2 C
10 The recombinants among the F2 progeny are those

e
m 1/2
C
/2 C am
R
1
et
with round seeds and green cotyledons and those with

g
es CW
1/4 CRCR
W
wrinkled seeds and yellow cotyledons.

1
1/4 CRCw 1/4 CRCW
1/4 CWCW
511

11 14 a)
Answers
parental (P)
homozygous parental (P)
homozygous homozygous
phenotypes: homozygous dwarf / potato
phenotypes: normal wing / vestigial wing /
tall / cut leaved leaved
normal body ebony body
genotypes: TTCC ttcc
genotypes: WWGG WWgg
(meiosis) (meiosis)
(meiosis) (meiosis)
gametes: TC tc
gametes: WG Wg
offspring (F1)
genotypes: TtCc
offspring (F1)
genotypes: WwGg
phenotypes: heterozygous
tall / cut-leaved
phenotypes: heterozygous
normal wing / normal body
F1 selfed TtCc TtCc
F1 selfed WwGg WwGg
(meiosis) (meiosis)
(meiosis) (meiosis)
gametes: TC Tc tC tc TC Tc tC tc
gametes: WG Wg wG wg WG Wg wG wg
TC
1/
4
4
TC
1/
1/
G
4
W
W
1/16 TTCC
1/
4
Tc
G
1/
4
4
Tc
1/
1/16 WWGG
1/
W
4
1/16 TTCc 1/16 TTCc
1/
W
4
tC
1/
4
g
tC
4
1/
1/16 WWGg 1/16 WWGg
1/
w
1/16 TtCC 1/16 TTcc 1/16 TtCC
4
1/
tc
w
4
4
1/
G
4
tc
1/
1/16 WwGG 1/16 WWgg 1/16 WwGG
1/
1/16 TtCc
w
1/16 TtCc 1/16 TtCc 1/16 TtCc
4
w
4
1/
g
1/16 WwGg 1/16 WwGg 1/16 WwGg 1/16 WwGg
1/16 Ttcc 1/16 ttCC 1/16 Ttcc
1/16 ttCc 1/16 ttCc 1/16 Wwgg 1/16 wwGG 1/16 Wwgg
1/16 ttcc 1/16 wwGg 1/16 wwGg
offspring (F2)
1/16 wwgg
phenotypes: tall / cut-leaved tall / potato dwarf / cut dwarf / potato
leaved leaved leaved offspring (F2)
phenotypes ratio: 9 : 3 : 3 : 1
phenotypes: normal wing normal wing vestigial wing vestigial wing
genotypes: 1 TTCC 1 TTcc 1 ttCC 1 ttcc
2 TtCC 2 Ttcc 2 ttCc phenotypes ratio: 9 : 3 : 3 : 1
2 TTCc
4 TtCc
genotypes: 1 WWGG 1 WWgg 1 wwGG 1 wwgg
2 WwGG 2 Wwgg 2 wwGg
12 a) BBSS, BBSs, BbSS or BbSs 2 WWGg
4 WwGg
b) From a test cross, using a spaniel that has a red
spotted coat. Among the puppies produced, the b) See diagram above.
presence of red coat or of spotted pattern indicates c) The recombinants are those with normal wings
that the other parent spaniel is heterozygous for and ebony bodies and those with vestigial wings
that character. and normal bodies.
13 A mutant organism (or cell) is one carrying altered
genetic material which makes it different from its
parent (or from its precursor cell).
512

15 First calculate the χ2 statistic. responsibility for the example answers to questions taken from
Answers
Predicted Observed Expected
Category ratio number, O number, E O−E (O − E)2 (O − E)2/E
1 a) Locus position of gene on chromosome; homozygous
Tall, axial 1 55 52 3 9 0.173 has two identical alleles of a gene.
flowers b) Parental phenotypes: (male) yellow fur, black nose X
Tall, 1 51 52 −1 1 0.019 (female) black fur, black nose
terminal Parental genotypes: Bbee X BbEe
flowers
Gametes: Be be X BE bE Be be
Dwarf, 1 49 52 −3 9 0.173
Offspring genotypes:
axial
flowers BE Be bE be
Dwarf, 1 53 52 1 1 0.019 Be BBEe BBee BbEe Bbee
terminal
be BbEe Bbee bbEe bbee
flowers
Total 208 208 0.384 Offspring phenotypes linked to genotypes:
So χ2 = 0.384 and there are three degrees of freedom. Fur Black Yellow Black Yellow
From a table of the distribution of χ2 (see page 366), Nose Black Black Black Black
the probability (P) of obtaining a deviation as large Fur Black Yellow Brown Yellow
as (or larger than) the one we have by chance alone Nose Black Black Brown Pale
falls between the probability levels of P = 0.90 and
P = 0.95. Ratio 3 : 3 : 1 : 1
This is not significant – there is no departure of the 2 a) Multiple alleles arise by gene nutation, which can
observed from the expected values. be caused by a change (substitution) in the base or
16 a) Liz and Diana nucleotide.
b) i) David and Anne b) Parental genotypes: CCaBb × ChCaBb
ii) James, William, Arthur and Fredrick Gametes: CB Cb CaB Cab × ChB Chb CaB Cab
c) 8 (Richard and Judith, Anne, Charles, Sophie,
Offspring phenotypes linked to genotypes:
Chris, Sarah and Gail)
d) James and William, Arthur and Diana, etc. ChB C aB Chb Cab
17 A dominant allele is expressed in all individuals that CB CChBB CCaBB CChBb CCaBb
inherit it (even if only heterozygous for that allele),
full black full black full full black
whereas a recessive condition appears only in offspring black
that are homozygous for that allele (and therefore with
parents who were both at least carriers of the allele – a Cb CChBb CCaBb CChbb CCabb
relatively rare event). full black full black full red full red
18 Gene mutations are due to changes in the sequence of CaB CaChBB CaCaBB CaChBb CaCabb
bases in the DNA of a gene, such as when one base is Him black albino black Him albino
replaced by another in the coding strand of DNA that black black
makes up the linear sequence of bases. Cab CaChBb CaCaBb CaChbb CaCabb
19 The genes controlling the production of the blood Him black albino black Him red albino red
proteins concerned in haemophilia are located on the
X chromosome. Haemophilia is caused by a recessive 3 a) Base substitution occurs when one base (adenine,
allele. As a result, haemophilia is largely a condition guanine, thymine or cytosine) is replaced by
of the male since in him a single X chromosome another. An example is the gene mutation that
carrying the defective allele (Xh Y) will result in causes sickle cell anaemia, where an adenine base
disease. For a female to have the haemophilia, she at one location is replaced by thymine.
must be homozygous for the recessive gene (Xh Xh), a b) Parental genotype HbA HbS HbA HbS
condition that is frequently fatal in utero.
Gametes HbA HbS HbA HbS
END OF TOPIC QUESTIONS HbA HbS
HbA HbA HbA HbA HbS
Cambridge Assessment International Education bears no HbS HbA HbS HbS HbS
513

5 The breeding of domesticated plants and animals has
Answers
Phenotype of offspring Ratio

created varieties with little external resemblances to
Normal 1
their wild ancestors. Darwin bred pigeons and noted
Sickle cell trait 2 there were more than a dozen, distinctive varieties of
Sickle cell anaemia 1 pigeon, all of which were descendents from the rock
dove (Figure 17.15). Darwin argued that if so much
c) In the population about 75% are homozygous
change can be brought about in so few generations,
for normal haemoglobin, just over 24% have the
then species must be able to evolve into other species
sickle cell trait and less than 1% are homozygous
by the gradual accumulation of minute changes as
for the HbS allele and have sickle cell anaemia.
environmental conditions alter and natural selection
People with sickle cell anaemia are more likely to
operates.
suffer from heart and kidney problems and can
be seriously ill. However, in areas where malaria 6 In natural selection, environmental factors act on
is common, having the sickle cell trait offers phenotypes so that organisms with the best suited
some protection against this disease since the phenotypes survive and breed, passing on the alleles
Plasmodium protozoan completes its life cycle in to their offspring. This leads to improved survival or
red blood cells but it cannot do so in red blood reproductive ability of these phenotypes and results in
cells that contain haemoglobin S. changes in the gene pool.
4 This is a self-assessment exercise – check your answer Artificial selection (selective breeding) is the
by referring to the answer to Question 4 on page 348, intentional breeding by humans for certain
Figures 16.5, 16.6 and 16.7 (pages 347–9) and the phenotypes or combinations of phenotypes. This
sections Genotype and phenotype (page 350) can lead to reduced ability to survive in the wild and
and How environment may affect the phenotype reduces the size of the gene pool.
(page 367). 7 Your ideas are likely to include:
» the identification of genes and alleles as Mendel’s
17 Selection and evolution factors
» chromosomes as vehicles for carrying genes
1 a) Your answer could include two of these soluble
» the behaviour of chromosomes in cell divisions
nutrients essential to phytoplankton growth:
nitrate; calcium or magnesium ions; » meiosis as the mechanism of separating alleles – so
b) The numbers of phytoplankton decrease rapidly that only one from each parent is passed on to the
in May and June due to the level of predation next generation.
by zooplankton and possibly due a shortage of 8 By evolution we mean the gradual development of
essential nutrients. life in geological time. For example, we know that
c) The increasing quantity of nutrients in October life appeared on Earth about 3500 million years ago
came from the decay of the dead phytoplankton and that most of the great diversity of living forms
and zooplankton. has appeared subsequently, with time. Before early
2 a) A non-native species may rapidly become the most geologist realised the Earth is extremely old, biblical
common species in a new environment due to an calculations suggested that life had been ‘created’ in
absence of established predators and parasites, and 4004 bc, or about 6000 years ago! If this were still
possibly due to limited competition for resources. believed, then there would be insufficient time for
b) Competition for food among the non-native evolution by natural selection.
population and the rapid spread of parasites 9 See Neo-Darwinism, page 402.
among them, particularly if their large numbers 10 A variety is a grouping within a species whose
cause them to live in close contact. members differ in some significant respect from
3 a) Peaks in predator populations occur after peaks other members of the species; a species is a group of
in the prey population. A rise in the number of organisms sharing morphological similarities that are
predators occurs because of the large number of reproductively isolated and can interbreed to produce
prey available to be caught and because fewer than fertile offspring. Different varieties of a species can
the maximum number of predators the habitat can interbreed.
support are competing for the prey. The examples you propose are most likely to be ones
b) An increases in the number of predators increases familiar in habitats near where you live.
the competition for food and predator numbers 11 The factors you are likely to suggest include:
exceed the supply of prey. Predators die so their
» Mutation – random, rare, spontaneous change in
population falls.
the genes in the gonads that lead to the possibility
4 See But gene pools do change, page 395.
514

of new characteristics in the offspring, that come to b) Continuous variation is the wide range of some
Answers
confer an advantage in the struggle for existence characteristics within a species, for example
» Selective predation of members of the population height. Continuous variation may be genetically
with certain characteristics that are genetically determined, or it may be due to environmental
controlled and genetic factors working together. A
» Emigrations of members of the population or characteristic such as height will show a normal
immigrations of members of other populations distribution curve, and is controlled by a group
» Sudden hostile physical condition, for example, of genes, called a polygene. The effects of any one
cold, flooding or drought, may quickly reduce a of these genes make a very small or insignificant
natural population to a very few survivors. On the effect on the phenotype, but the combined effect
return of a favourable environment, the numbers of all the genes of the polygene is to produce
of the affected species may return to normal, for a wide variety among the offspring in height.
example, due to reduced competition for food Environmental factors, such as temperature,
sources. However, the new population has been built amount of available water, disease and type of soil,
from a very small sample of the original population, will also affect how the genotype is expressed.
so there are likely to be more crosses between closely 3 a) S. angelica is an example of an organism with
related individuals (resulting in fewer heterozygotes more than one sets of chromosomes, a polyploid.
and more homozygotes) and some alleles may be lost Polyploidy is largely restricted to plants and
altogether. (This is called random genetic drift.) animals that reproduce asexually. The additional
» A barrier may develop within a population, instantly set of chromosomes can come from a member
isolating a small sample of the original population, of the same species (autopolyploidy) but in this
which may carry an unrepresentative selection of case it came about by the hybridisation of two
the gene pool, yet be the basis of a new population. related species (allopolyploidy). The chromosome
(This is another form of genetic drift. It is called the sets of S. maritima (AA genome) and S. alterniflora
founder effect.) (BB genome) originally combined to create the
chromosome set of S. townsendii (AB genome),
END OF TOPIC QUESTIONS which is sterile (as it has 61 chromosomes and so
These answers are for guidance only. They do not represent meiosis is disrupted) and spreads vegetatively. But
the full response required by questions in the examination. then chromosome doubling occurred to produce
Cambridge Assessment International Education bears no S. angelica (AA BB genome), which is fertile.
responsibility for the example answers to questions taken from b) The cultivated potato has double the number of
its past question papers which are contained in this publication. chromosomes of the smaller wild potato.
4 a) The gene pool is all the genes (and their alleles)
1 a) 46.5–47% (q2 = 0.4; p = 0.368)
present in a breeding population. The probability
b) Answers may include: in small populations;
that an organism will die before a certain stage
with asexual reproduction; if a mutation occurs;
varies – this is differential mortality. The possession
if mating is not random; if there is emigration
of a particular allele or combination of alleles may
or immigration from of the population; if there
make it more likely that an individual will survive,
is a selective pressure, meaning that one of the
breed and pass on its particular alleles.
genotypes is not expressed in the expected ratio;
b) Stabilising selection is a mechanism which maintains
for a haploid organism.
favourable characteristics and the alleles responsible
2 a) This is selection caused by humans and is a for them, and eliminates extremes and abnormalities
deliberate and planned process, selecting for the that are harmful. An example is the birth weights
largest ear or the most number of grains in the of human babies between 1935 and 1946 (see
ear, or best disease resistance for example (or a Figure 17.8, page 389). Since variation is reduced,
combination of these characteristics). The best of the evolutionary change is less likely to happen.
progeny showing these particular characteristic(s) c) Directional change occurs when environmental
are used as the next generation of parents. Offspring conditions change. Under the new conditions, the
showing less desired features are removed from the majority of organisms may no longer be well suited
breeding population. Over several generations, this to their environment so individuals with alternative
leads to deliberate genetic change. The frequency phenotypes may have a competitive advantage.
of the required alleles increases rapidly in the An example is the development of resistance to
population. Starting from ancestor grasses, this is antibiotics by bacteria (see Figure 17.9, page 390).
how modern-day wheat crops have developed much d) Disruptive selection occurs when particular
larger yields, better pest and disease resistance, environmental conditions favour the extremes of
shorter stiffer stalks, etc. a phenotypic range over intermediate phenotypes.
515

An example is grasses that have developed a of predators when population new/low in
Answers
resistance to toxic metals so are able to grow on numbers)

contaminated land but are now unable to grow on » on subsequent stabilisation of population
uncontaminated land. Grasses that do not have numbers (balance between reproduction/
the resistance are able to grow on uncontaminated predation pressures, the idea of carrying
land but not on contaminated land. The two capacity for that habitat).
varieties can interbreed since they are wind- 8 The Simpson Diversity Index for this habitat:
pollinated but intermediate forms do badly in both
types of environment. Species (no of
individuals) n n−1 n(n − 1)
Groundsel 45 44 1980
18 lassification, biodiversity and
C Shepherd’s purse 40 39 1560
conservation Dandelion 10 9 90
1 The central column needs to start with ‘Domain: one Total (N) 95
of the three major forms of life’. The left- and right-
hand columns need to parallel this addition with ∑ n (n −1) = 1980 + 1560 + 90 = 3630
‘Domain: Eukaryota’. 94 8930
D = 95 × = = 2.46
2 Precisely defined and internationally agreed scientific 3630 3630
names facilitate cooperation between observers by 9 The original data in Figure 18.22 were obtained by a team
identifying the exact species that is being investigated of pre-University students in an activity they designed
and reported on. and carried out (independently of teachers) as the
3 Possible abiotic factors include light, humidity, topography, culmination of a field course. Respond to this question
soil (pH, moisture content, organic matter, etc.) in like-manner. Select two small teams of students, each
to tackle the calculation of one of the diversity indices.
4 a) ecosystem
Then, by group discussion, evaluate the effect of age/stage
b) population
of dune development on diversity. Present your data and
c) abiotic factor
conclusions as a poster or display newspaper item.
d) community
e) habitat 10 The chief ecosystems are:
f) abiotic factor » Tundra, e.g. alpine tundra, which occurs on the
g) biomass highest mountains, well above the tree-line
5 » Grassland, e.g. steppe, prairie and pampas, or
Plant Animal
savannah, which is tropical grassland
A high water location Spiral wrack Rough winkle » Desert
A low water location Oar weed Acorn barnacle » Forest or scrubland
6T he estimated population size would be halved, 11 Human actions and activities that represent a threat to
i.e. 40/2 = 20. the Earth’s wildlife include:
7 a) The size of the population at days 2, 16, 31 and 46 » Deforestation – Destruction of trees destroys the
and 76: habitats of numerous species of animals, plants, fungi
Day n1 × n2 / m2 N
and bacteria which therefore decline in numbers.
» Desertification – This is speeded up by:
2 7×6/2 21
– overgrazing of land,
16 14 × 12 / 2 84
– deforestation, or
31 25 × 24 / 3 200
– climate change.
46 19 × 16 / 2 152
» Excessive application of pesticides in modern
76 19 × 14 / 2 133
industrial agriculture. Pesticides have improved
b) Plot the graph using an Excel spreadsheet – productivity in agriculture, but their use has
concerning ‘time in days’ and ‘N’, which will you reduced biodiversity.
plot on the x and the y axis? » Air pollution – The levels of carbon dioxide in the
c) The annotations to the curve are an opportunity to atmosphere have been rising since the Industrial
speculate on: Revolution in the developed countries of the world.
» on the initial rapid rise in numbers (continuing This gas is a major contributor to global warming
immigrations, initial absence of competition and destructive climate change.
for abundant resources, lack of presence » Water pollution.
516

12 16
Answers
parental genotype Captive breeding
programmes of zoos and
gene mutations chromosome mutations
in gamete - in gamete-producing
Terrestrial and aquatic seed banks at botanical
producing cells cells nature reserves gardens
Habitats that are Originally, zoos were
mutations already rare are collections of largely
especially vulnerable to unfamiliar animals kept
natural disaster – rare for curiosity, with little
changed genotype habitats themselves are concern for any stress
easily lost, if a range caused, but now captive
independent assortment + crossing
over of examples are not breeding programmes make
production of preserved as nature good use of these resources
gametes - reserves
meiosis
When a habitat Captive breeding maintains
disappears the whole the genetic stock of rare
mate selection
and random
community is lost, and endangered species
fertilisation threatening to increase
the total number of
endangered species
gamete
gamete A refuge for endangered The genetic problems
wildlife allows these arising from individual
fertilisation
species to lead natural zoos having very limited
lives in a familiar numbers to act as parents
environment for which is overcome by inter-zoo
new individual
(new genotype) they are adapted and to co-operation (and artificial
be a part of their normal insemination in some
food chains cases)
growth and
development of The wildlife of a reserve Animals in zoos tend to
zygote into new may be monitored for have significantly longer
individual
early warning of any life expectancies and are
further deterioration in available to participate
impact of environment
numbers of a threatened in breeding programmes
phenotype
species so that remedial for much longer than wild
steps can be taken animals do
The offspring of Captive breeding problems,
13 Information may be available from local wardens or endangered species are for most species it is
rangers via their head office. nurtured in their natural applied to, have been
14 in vitro refers to biological processes occurring in cell environment and gain highly successful, although
extracts (literally ‘in glass’); in vivo refers to biological all the experiences the young do not grow up
processes occurring in living organisms (literally this normally brings, in the ‘wild’, so there is
‘in life’). including the acquisition less opportunity to observe
of skills from parents and learn from parents and
15 Possible answers:
and peers around them peers
» The possibility of artificial insemination using sperm
There is an established Breeding programmes
obtained from captive individuals from a different
tradition of maintaining generate healthy
gene pool. Similarly, in-vitro fertilisation and the
reserves and protected individuals in good
implantation of embryos in surrogate mothers areas in various parts numbers for attempts at
» Maintenance of accurate breeding records so that of the world, so there re-introduction of
the genetic relatedness of progeny is known for is much experience to endangered species
future crosses and prior to exchanges of gametes or share on how to manage to natural habitats, a
individuals between different zoos them successfully particularly challenging
» Monitoring of the health and development of process given that natural
progeny and on-going supervision of the success of predators abound in these
methods of release back into the wild to minimise locations
immediate predation of released stock.
517

as these are in turn eaten by zooplankton there
Answers
Captive breeding
programmes of zoos and is bioaccumulation of the toxins. Since whales
Terrestrial and aquatic seed banks at botanical consume huge quantities of these small organisms,
nature reserves gardens there will be high concentrations of these
chemicals in their system. The chemicals are lipid
Nature reserves are popular Zoos and botanical gardens
sites for the public to are accessible sites for soluble, and are stored in the whale’s fat deposits.
visit (in approved ways), the public to visit (as They are not broken down.
thereby maintaining they are often situated in e) i) By acting on the voltage-gated sodium channels
public awareness of the urban settings where many in neurones, saxitoxin prevents nerve impulses
environmental crisis due to may have access), so they from happening by stopping the nerve cell
extinctions and individual contribute effectively to membrane from depolarising. This will result
responsibilities that arise public education on the in death.
from it environmental crisis ii) They are unicellular organisms with flagella.
Reserves are ideal venues to Seed banks are a convenient 2 a) An endangered species has a low population
which to return endangered and efficient way of number and is in danger of becoming extinct.
individuals, the products maintaining genetic b) An endangered species, such as the squirrel
of captive breeding material of endangered monkey, can be protected by habitat preservation,
programmes, providing plants, as they may exploit such as setting up nature reserves or national
realistic conditions for the ways seeds survive long parks, and measures such as the banning of
re-adaptation to the periods in nature hunting. Captive breeding programmes could
habitat but facilitating the also be set up in zoos, and could include assisted
monitoring of the reproduction using IVF.
re-introduction
3 a) i) 0.03
17 The stocks in seed banks must be viable. Over very ii) Table 3.1 shows that in Sulawesi, there is a
long periods, viability of seeds decreases, so fresh high density of humans and a low density of
formed seeds are needed regularly. Also, genetic macaques. In Bacan, there fewer humans per
viability is maintained by this process because new square kilometre and a much greater number of
seeds are the products of sexual reproduction and so macaques. This suggests that humans compete
maintain the diversity of the gene pool. with macaques for space, or may take over
their environment, or destroy their habitat.
END OF TOPIC QUESTIONS They may kill macaques, either intentionally or
These answers are for guidance only. They do not represent by causing disease in the macaque population.
the full response required by questions in the examination. b) Answers may include: establish reserves;
Cambridge Assessment International Education bears no ban hunting trade; set up a captive breeding
responsibility for the example answers to questions taken from programme to increase the population size and
its past question papers which are contained in this publication. release offspring into the wild; educate the human
population about the macaque and how to protect
1 a) Biodiversity is the diversity and abundance of the species; monitor and treat disease within the
different species within a habitat, and at a genetic macaque population; ring-fence the macaque
level the range of alleles within a species. territories and stop development in those areas.
b) i) genes, environment
ii) Whales live deep underwater, and migrate over
large distances. 19 Genetic technology
c) Because the St Lawrence river runs through
1 Viral DNA takes over the ribosomal machinery of the
busy industrial areas, it is likely that the water is
host cell, causing the production of viral proteins that
polluted, or there is industrial contamination. This
are enzymes. Viral enzymes cause the replication of
will not only affect the whale population, but also
viral DNA and the production of other molecules that
their prey, so there may be reduced food for the
make up new viruses (see Figure 10.19, page 214).
whales. Whales may be injured or killed by the
many boats passing along the river, or the engine 2 a) See Nucleic acids – the information molecules,
noise or propeller vibrations may affect the whales, pages 120–2, and Figure 6.4, page 123.
as they communicate by sonar. b) See Table 19.1, page 459.
d) DDT and PCBs accumulate through the food 3 a) A sticky end consists of a short sequence of exposed
chain. They are industrial chemicals that are bases of unpaired nucleotides forming a single-
washed into the rivers and seas. They are ingested stranded extension at the end of a length of DNA.
by the primary producers, the phytoplankton, and It is created by the action of a particular restriction
518

endonuclease that recognises a specific base They may also add even more to human nutrition by
Answers
sequence in a length of DNA and cuts the DNA in helping to the overcome protein deficiency as well as
this distinctive way. See also Figure 19.4, page 462. meeting calorie needs.
b) Sticky ends attach to each other by complementary 9 Many newspaper reports are often rather superficial.
base pairing. They are held together by the formation You may have to amplify the criticisms slightly in
of hydrogen bonds between complementary bases. order to be able to introduce balancing arguments.
The enzyme ligase then catalyses the formation Your own opinion needs stating simply, with one or
of C–O bonds between the sugar–phosphate two clearly explained reasons.
backbones of the two DNA strands.
10 Flowering plants are a major component of human
4 a) See Table 16.2, page 357. diets and very many are insect-pollinated. Honey bees
b) See Table 19.1, page 459. and butterflies are some of these insect pollinators.
c) The bacterial chromosome is a single circular A reduction in their numbers would lead to fewer
molecule of DNA within the cytoplasm, but seeds being formed. The supply of fruits and seeds for
attached to the cell surface membrane at one cultivation and as food would be threatened.
point. Plasmids are tiny circular molecules of
DNA, free-floating in the cytoplasm of some END OF TOPIC QUESTIONS
bacteria. They replicate independently of the
bacterial chromosome.
5 The genes of prokaryotes are generally easier to modify Cambridge Assessment International Education bears no
than those of eukaryotes because: responsibility for the example answers to questions taken from
» prokaryotes have a single, circular chromosome, so its past question papers which are contained in this publication.
only one copy of a gene has to be engineered into
1 a) Genetic screening could identify women who
their DNA, whereas eukaryotes have two alleles of
are carriers (have the recessive allele). With
every gene
counselling, they could choose not to have
» plasmids, the most useful vehicle for moving children, or if they do choose to have children
genes, occur in prokaryotes but mostly do not any male embryos that have the allele could be
in eukaryotes – the exceptions are some fungi, aborted, or embryos without the allele could be
including yeast, and a few plants preselected and implanted.
» transcription of DNA into RNA in prokaryotes does b) i) Gene therapy is a technique that attempts
not require the removal of ‘non-informative DNA’ to use genes to treat or prevent disease by
(introns), but in eukaryotes it does inserting a gene into a patient’s cells instead
» bacterial walls can be crossed by plasmids (after of using conventional medicine or surgery.
suitable treatments). The aim of the gene therapy is to increase the
6 A mutant allele is one of a pair of alleles in which patient’s quality of life or to give them a normal
(exceptionally) there has been a change in the life expectancy, e.g. people with cystic fibrosis
structure of the DNA. Typically this involves a single or people with inherited eye disease.
base substitution, a translocation, a transposition or ii) It is caused by a recessive allele and is a serious
an insertion or deletion of a base or short sequences of (and widespread) disease.
bases. c) i) F8 gene is harder to insert into the vector as
7 A person with a single allele for cystic fibrosis is a it is much longer (> 8 kilobases), making it
‘carrier’ and does not express the disease; whereas difficult for it to enter the nucleus
someone with a single allele for Huntington’s disorder ii) The advantages of using an adenovirus rather
will become affected by the disease eventually. than a retrovirus as a vector: it has double-
stranded DNA so the stage of making cDNA
8 The fruits of the cereals (which include wheat and rice)
is not required, high gene expression so more
are the staples of human diets all over the world. They
therapeutic protein. Disadvantages: high
provide the bulk of essential energy- rich foods. The
immune response unlike retrovirus, so there
ability of leguminous plants to fix atmospheric nitrogen
is more likely to be side effects; it may also be
for amino acid and protein production enable these
removed before it reaches the target cells.
plants to grow well without the addition of (expensive)
nitrogen-based fertilisers. It also makes food products 2 a) Because it is caused by a single, recessive gene, so
from them (peas and beans, for example) relatively rich the addition of a dominant allele could cure the
in proteins. Cereals that are genetically modified so condition. The dominant allele only needs to be
that they could also fix nitrogen (if they were created) added to a few cells. It is a serious condition so it
would grow well without nitrogen-based fertilisers. is worth taking risks to try to cure it.
519

b) The adenoviruses would contain the dominant The DNA samples are placed in wells in the gel
Answers
allele RPE65 and would no longer contain genes and covered with a buffer solution. The phosphate
that cause respiratory infections. groups in DNA give it a net negative charge so
c) Because the condition is relatively rare, the side in the electric field the DNA fragments migrate
effects are not known and it is an expensive towards the positive pole. In electrophoresis,
treatment. separation occurs according to the size of the
3 a) Restriction endonucleases occur in the cytoplasm molecule and the charge carried.
of bacteria and cut DNA molecules into shorter b) i) Variable number tandem repeats are short
lengths. DNA ligase occurs in the nuclei of sequences of DNA that do not code for
organisms and catalyses the joining of sugar– proteins. They are regions where short
phosphate subunits to form the backbone of DNA sequences of bases are repeated many times.
strands. DNA polymerase occurs in the nuclei of They make up between 10% and 25% of
organisms and brings about DNA replication when our total DNA. We inherit a distinctive
small strands of DNA are mixed with the four combination of these repeat regions, half from
nucleotides. Reverse transcriptase is produced by our mother and half from our father, and
retroviruses and is used to make complimentary each of us has a unique sequence (apart from
DNA from mRNA. identical twins).
b) mRNA for human insulin production is extracted ii) A sample of cells is obtained from blood,
from human pancreas cells by isolating the semen, hair root or body tissue and the DNA
ribosomes. Using reverse transcriptases, a DNA extracted. If necessary, it can be increased
copy of the gene for insulin can be produced. using the polymerase chain reaction. The DNA
This gene is then spliced into DNA that can be is cut into small double-stranded fragments
introduced into a bacterium, such as appropriate using restriction enzymes, and the fragments
stains of E. coli, and then the bacterium can be are separated using gel electrophoresis. The
induced to synthesise human insulin. (See Figure double strands are separated into single
19.2, page 460.) strands; they are then transferred to a
c) i) The gene for insulin is difficult to extract membrane and radioactively labelled probes
from human pancreatic tissue and contains added. The membrane is overlaid with X-ray
introns as well as the coding sections. The film which becomes selectively fogged by
mRNA complementary to the gene for insulin emissions from the radioactive probes. When
is relatively easy to extract and can be used to the film is developed it shows the positions of
synthesise a version of the gene that contains the DNA fragments and has the appearance
only the coding sections. of a bar code.
ii) Animal insulin is derived from cows and c) DNA profiles can be used to identify criminals
pigs. Some people object on religious or other suspected of murder, rape or burglary, and to
grounds and some people may have a reaction identify corpses that are very decomposed or
against it. People are less likely to react against where only small parts of the body remain. They
human insulin as it is chemically identical to can also be used to establish paternity. DNA
the body’s own insulin. profiling has been used in the study of wild
animals to identify unrelated animals for captive
4 a) Electrophoresis is carried out on an agarose gel
breeding programmes.
or polyacrylamide gel, both of which contain tiny
5 This is a self-assessment exercise – check your answer
pores that act as a molecular sieve. Small particles
by referring to Genetically modified organisms in
can move quickly through the gel whereas larger
agriculture (pages 482–5).
molecules move more slowly. A power supply is
used to create an electric field across the gel.
520

Glossary
Glossary
Active immunity immunity resulting from exposure to an cell disorder, the phenotype of a person who has HbA HbS is
antigen. During the subsequent immune response, antibodies the less severe sickle cell trait and the phenotype of a person
are produced by plasma cells and the body makes memory who has HbS HbS is the more severe sickle cell anaemia.
cells that provide ongoing long-term immunity. There is a Community all of the populations of all of the different species
delay before the immune response is complete, so immunity within a specified area at a particular time.
takes some days to build up.
Condensation reaction the formation of larger molecules involving
Allele frequency the commonness of the occurrence of any the removal of water from smaller component molecules
particular allele in a population.
Diffusion the net movement of particles such as molecules from
Allele one of two or more alternative nucleotide sequences at a region where they are at a higher concentration to a region
a single gene locus, so alleles are variant forms of a gene. with a lower concentration, using energy from the random
For example, the alleles of the ABO blood group gene are movements of particles. This includes diffusion of small
found at a locus on chromosome 9, with the alleles including non-polar molecules (such as oxygen and carbon dioxide)
I A, IB and IO. Diploid body cells contain two copies of each through the cell surface membrane, as well as diffusion of
homologous chromosome, so have two copies of chromosome fat-soluble molecules (such as vitamin A) through the cell
9, and so have two copies of the gene. These may be the surface membrane.
same allele (homozygous), for example IA IA, or IB IB or
Diploid a eukaryotic cell or organism containing two complete sets
IO IO, or they may be different alleles (heterozygous), for
of chromosomes (two copies of each homologous chromosome),
example IA IB, or IA IO or IB IO. The gene for producing the
shown as 2n, such as a human body (somatic) cell.
haemoglobin _-polypeptide has a number of alleles. Two of
these are the normal allele, HbA, and the sickle cell allele, Disaccharide a sugar that is a condensation product of two
HbS, giving HbA HbA and HbS HbS as homozygous genotypes monosaccharides, e.g. maltose.
and HbA HbS as a heterozygous genotype. Disease an abnormal condition affecting an organism, which
Antibody a glycoprotein secreted by a plasma cell. An antibody reduces the effectiveness of the functions of the organism.
binds to the specific antigen that triggered the immune Dominant an allele with a phenotype that is expressed even
response, leading to destruction of the antigen (and any when present with an allele that is recessive to it. For
pathogen or other cell to which the antigen is attached). example, in the ABO blood group gene, IA is dominant to IO.
Antibodies have regions that vary in shape (variable regions) Therefore, a person with the genotype IA IO has blood group
that are complementary to the shape of the antigen. Some A because only the dominant allele is expressed.
antibodies are called antitoxins and prevent the activity of Ecosystem a unit made up of biotic and abiotic components
toxins. interacting and functioning together, including all the living
Antigen a protein (normally – some carbohydrates and other organisms of all types in a given area and all the abiotic
macromolecules can act as antigens) that is recognised by physical and chemical factors in their environment, linked
the body as foreign (non-self) and that stimulates an immune together by energy flow and cycling of nutrients. Ecosystems
response. The specificity of antigens (which is a result of the may vary in size but always form a functional entity: for
variety of amino acid sequences that are possible) allows for example, a decomposing log, a pond, a meadow, a reef, a
responses that are customised to specific pathogens. forest or the entire biosphere.
Artificial immunity immunity that is acquired by a person as a Endocrine gland a gland containing specialised secretory cells
result of medical intervention. This includes artificial passive that release a hormone into the bloodstream at a distance
immunity following injection of antibodies (for example from the hormone’s target organ.
monoclonal antibodies, to treat acute life-threatening Endocytosis the uptake of materials into cells by inward foldings
infections, such as tetanus or rabies). It also includes of the cell surface membrane to form sacs of membrane that
the long-term immunity that results from the injection of separate from the membrane to form vesicles within the
antigens (such as those attached to killed or weakened cytoplasm, using energy from ATP to move the cytoplasm
pathogens) where memory cells are made. around. The process may involve liquid solutions or suspensions
Biodiversity the total number of different species living in (pinocytosis) or solid macromolecules or cells (phagocytosis).
a defined area, ecosystem or biome. It is also possible to Eukaryotic (cells) cells with a large obvious nucleus, e.g. the
consider the biodiversity of the Earth. cells of animals, plants, fungi and protocista; a eukaryote is
Cellular respiration the controlled transfer of energy from an organism with eukaryotic cells.
organic compounds in cells to ATP. Excretion the elimination from the body of waste compounds
Codominant alleles that are both expressed if they are present produced during the metabolism of cells, including, for a
together in a heterozygous organism. For example, alleles human, carbon dioxide (excreted through the lungs) and urea
IA and IB of the ABO blood group gene are codominant. (excreted through the kidneys in urine).
Therefore, in a heterozygous person, IA IB, both alleles are Exocytosis the secretion of materials out of cells by cytoplasmic
expressed and the blood group is AB. In the case of the vesicles fusing with the cell surface membrane and releasing
haemoglobin–polypeptide gene, codominance means that the the contents of the vesicle into the fluid around the cell,
phenotype of a person who has HbA HbA is unaffected by sickle using ATP to move the cytoplasm.
521
482876_EM_Biology_521-534.indd 521 22/02/20 11:53 AM

Facilitated diffusion the diffusion of ions and polar (water- Infectious disease a disease caused by a pathogen that can be
Glossary
soluble) molecules through cell membranes using specific transmitted from one host organism to another.
protein channels or carriers, down a concentration gradient Locus the position of a gene or other specific piece of DNA (such
(from regions where they are at higher concentration to as a marker) on a chromosome. The same gene is always
regions where they are at lower concentration). found at the same locus of the same chromosome (unless
Gene a sequence of nucleotides that forms part of a DNA there has been a mutation). The locus is designated by the
molecule. chromosome number, its arm, and its place. For example,
Gene pool all the genes and their different alleles, present in an the gene associated with ABO blood groups is at locus 9q34,
interbreeding population. meaning the gene is found on chromosome 9, on the long
arm (q) at region 34. The gene associated with sickle cell
Genetic dictionary a list of the particular base sequences
anaemia is at locus 11p15.5, meaning chromosome 11, short
that correspond with particular amino acids. This will vary
arm (p), region 15.5.
depending on whether messenger RNA, transfer RNA or either
of the two DNA base sequences is given. Macromolecule very large organic molecule (relative
molecular mass: 10 000+), e.g. proteins, nucleic acids or
Genotype the particular alleles of a gene at the appropriate locus
polysaccharides.
on both copies of the homologous chromosomes of its cells
(for example, IA IB). It is sometimes described as the genetic Magnification the size of an image of an object compared to the
constitution of an organism with respect to a gene or genes. actual size. It is calculated using the formula M = I ÷ A (M is
magnification, I is the size of the image and A is the actual
Glycosidic bond a type of chemical linkage between
size of the object, using the same units for both sizes).
monosaccharide residues in polysaccharides.
This formula can be rearranged to give the actual size of an
Habitat the particular location and type of local environment object where the size of the image and magnification are
occupied by a population or organism, characterised by its known: A = I ÷ M.
physical features or by its dominant producers (such as rocky
Monomer a small molecule that is linked with many others of the
shore or sugar cane field).
same type to form a polymer, e.g. glucose, amino acids.
Haploid a eukaryotic cell or organism containing only one
Monosaccharide a simple carbohydrate (all are reducing sugars).
complete set of chromosomes (only one of each homologous
pair of chromosomes), shown as n, such as a human sperm or Natural immunity immunity that is acquired by the individual
secondary oocyte. as a natural part of their life. This includes natural passive
immunity following transfer of maternal antibodies into a
Heterozygous a term describing a diploid organism that has
fetus through the placenta and into a newborn infant in the
different alleles of a gene at the gene’s locus on each of
first milk (colostrum). It also includes the natural active
the homologous chromosomes in its cells (e.g. HbA HbS) and
immunity that follows natural infection by a pathogen
therefore produces gametes with two different genotypes
involving the production of memory cells (for example,
(12 HbA and 12 HbS). A heterozygote is an organism that is
natural infection with chicken pox, giving long-term
heterozygous.
protection against this virus).
Homologous pair chromosomes in a diploid cell occur in
Niche the functional role or place of a species of organism
homologous pairs, each chromosome contains the same
within an ecosystem, including interactions with other
sequence of genes but they are derived from different
organisms (such as feeding interactions), habitat, lifecycle
parents.
and location, adding up to a description of the specific
Homozygous a term describing a diploid organism that has the environmental features to which the species is well adapted.
same allele of a gene at the gene’s locus on both copies of
Non-infectious disease a disease with a cause other than a
the homologous chromosomes in its cells (e.g. HbA HbA) and
pathogen, including genetic disorders (such as sickle cell
therefore produces gametes with identical genotypes (all
anaemia) and lung cancer (linked to smoking and other
HbA). A homozygote is an organism that is homozygous.
environmental factors).
Immune response the complex series of reactions of the body
Non-reducing sugar a sugar that does not has a free aldehyde or
to an antigen, such as a molecule on the outside of a
ketone so it cannot act as a reducing agent, e.g. sucrose is a
bacterium, virus, parasite, allergen or tumour cell.
non-reducing sugar.
» The immune response begins with an innate first Organelle a unit of cell substructure.
response, carried out by phagocytic white blood
cells, which can destroy and engulf (by phagocytosis/ Osmosis the diffusion of water molecules from a region where
endocytosis) many different foreign organisms. water is at a higher water potential through a partially
permeable membrane to a region with a lower water
» At the same time, the primary phase of the adaptive potential.
immune system response begins, in which specific
clones of B-lymphocytes and T-lymphocytes divide and Passive immunity immunity involving the transfer of antibodies
differentiate to form antibody-secreting plasma cells (already made in the body of another organism or in vitro)
(from B-lymphocytes) and T helper cells and T killer cells into the body where they will bind to their specific antigen
(from T-lymphocytes) that are specific to the antigen, if it is present. This gives instant immunity but does not lead
contributing to its destruction or preventing its activity. to the development of memory cells, so the immunity only
lasts for a few weeks.
» This leads into the secondary phase of the adaptive
immune system response, where memory cells retain the
capability to secrete antibodies or act as T helper or T killer
cells as soon as the specific antigen is detected again.
522

Pathogen a biological agent (such as a virus, bacterium, fungus Resolution the ability of a microscope to distinguish two
Glossary
or protoctist) that causes disease. A pathogen causing objects as separate from one another. The smaller and closer
human diseases will have, as part of its structure, proteins together the objects that can be distinguished, the higher
that are different from those of the human host and are the resolution. Resolution is determined by the wavelength
therefore antigens. of the radiation used to view the specimen. If the parts
Phenotype the physical, detectable expression of the particular of the specimen are smaller than the wavelength of the
alleles of a gene or genes present in an individual. It may radiation, then the waves are not stopped by them and they
be possible to see the phenotype (e.g. human eye colour) are not seen. Light microscopes have limited resolution
or tests may be required (e.g. ABO blood group). When the compared to electron microscopes because light has a much
phenotype is controlled by a small number of alleles of longer wavelength than the beam of electrons in an electron
a particular gene, it may be genetically determined (e.g. microscope.
human eye colour), giving rise to discontinuous variation. Saltatory conduction the propagation of action potentials along
When the phenotype is controlled by the additive effects myelinated axons from one node of Ranvier to the next node,
of many genes (polygenic), it may be affected by the increasing the conduction velocity of action potentials.
environment as well as genes (e.g. human height), giving Self the products of the body’s own genotype, which contain
rise to continuous variation. proteins (normally – some carbohydrates and other
Polymer a large organic molecule made up of repeating subunits macromolecules can act as antigens) that do not trigger an
(monomers). immune response in the body’s own immune system. Inside
Polysaccharide very high molecular mass carbohydrates, formed the body that produced them, self proteins do not act as
by condensation of vast numbers of monosaccharide units, antigens (and so do not stimulate an immune response) but,
with the removal of water. if introduced into another body, they become non-self.
Population all of the organisms of one particular species within Species a group of organisms of common ancestry that closely
a specified area at a particular time, sharing the same gene resemble each other structurally and biochemically. Their
pool and more or less isolated from other populations of the morphological (structural) similarities are often used to
same species. identify which species they belong to. They are members
of natural populations that are actually or potentially
Pressure the pascal (Pa) and its multiple the kilopascal (kPa) are
capable of breeding with each other to produce fertile
generally used by scientists to measure pressure. However,
offspring, and which do not interbreed with members of
in medicine the older unit, millimetres of mercury (mmHg) is
other species.
still used (1 mmHg = 0.13 kPa).
Transpiration the process through which water vapour is lost
Prokaryotic (cell) cells without a true nucleus (they have a ring
from the aerial parts of plants. It occurs as the result of
of RNA or DNA as a chromosome); a prokaryote is a small,
evaporation of water at the surface of mesophyll cells into
unicellular organism without a true nucleus, e.g. bacteria.
the airspaces within the leaf, followed by diffusion of water
Recessive an allele with a phenotype that is not expressed when vapour out of the leaf, mainly through stomata, down a water
an allele that is dominant to it is present. For example, IO potential gradient from the surface of spongy mesophyll
is recessive to IA, so a person with the genotype IA IO has cells via airspaces in the leaf to the atmosphere.
blood group A, and a person can only be blood group O if
Vaccination the medical giving of material containing antigens,
they are homozygous recessive, IO IO.
but with reduced or no ability to be pathogens, in order to
Reducing sugar a sugar that has a free aldehyde or ketone that give long-term active immunity as a result of the production
can act as a reducing agent, e.g. glucose and fructose are of memory cells.
reducing sugars.
523

Index
Index
A amino acids 48, 58 ATP–ADP cycle 22, 242

deamination 302 ATP synthase (ATPase) 252
abiotic environment 387, 413 DNA triplet codes 130–1 atria (singular: atrium) 180, 181, 186
ABO blood group system 356 amino group 48 atrial systole 182–3
abscisic acid (ABA) 314, 315, 337 amniocentesis 476 atrioventricular node (AV node) 184, 186
absorption spectrum, chlorophyll 274 Amoeba 2, 7, 421 atrioventricular valves 181
accidents 202 contractile vacuole 97 autolysis 18
acetylcholine (ACh) 326, 331 amylase 70 autosomal chromosomes 357
acetyl coenzyme A 251 amylopectin 40 autotrophic nutrition 240, 270, 281
actin 255, 331, 333–4 amylose 40 auxins 337, 339, 341
action potential 324–5, 341 anabolic reactions 61 axons 319–20
all or nothing principle 325 anaerobic respiration 259–61, 265 Azolla 263
speed of conduction 326 anaphase
action spectrum, chlorophyll 274
activated B-lymphocytes 228, 229
meiosis 346, 347, 348 B
mitosis 116, 117 bacteria 417–18
activation energy, effect of enzymes animal cells 13–14, 21
63–4 antibiotic resistance 217–21, 390
gas exchange 188 Escherichia coli 2, 23–4, 459
active immunity 236 osmosis 96–7
active sites 64, 102 extremophiles 417, 425, 459
Animalia 416, 424, 455 structure 24–5
active transport 87, 98–100, 103, 142 antibiotic resistance 217–19, 390
neurones 323 bacterial conjugation 217–8
consequences 220 bacterial diseases 201–4, 208–11, 222
proximal convoluted tubule 306 management 221
adaptations 265 balanced polymorphism 392
antibiotics 216, 222 balancing selection 391
rice 261–2 development of new drugs 220
xerophytes 157–8 base addition mutation 138
mechanisms of action 217 base deletion mutation 138
adenine 121 antibodies 238
adenosine deaminase (AD) 473 base substitution mutation 138, 369–70
monoclonal 232–5 BCG (Bacillus Calmette–Guérin) vaccine
adhesion, water 154–5 production of 228–30
adipose tissue 46 209–10
structure 231–2 behavioural separation 410
ADP (adenosine diphosphate) 22 anticodons 130, 133, 134, 135, 139
adrenal glands 318 belt transects 433, 434
antidiuretic hormone (ADH) 308–10, 318 Benedict’s test 31–2
aerenchyma tissue 261, 262, 265 antigen–antibody reaction 228–30
aerobic respiration 249–57, 265 semi-quantitative use 34–5
antigen presentation 228, 229 benign tumours 114
comparison with anaerobic respiration antigens 212, 225–6
260 Bent grass 408
aorta 167, 168, 170, 181 b-sheets 50
agriculture apoplast pathway 151, 152
genetic diversity 446 bicuspid valve 181
aquaporins 85, 310 bilayer, cell surface membrane 82–3, 98
genetic engineering 482–5 Archaea 417–18
see also food crops binary fission 23
arrhythmia 186 binding proteins 102
AIDS 212–15 arteries 168–70
alarm substances 224, 226 binding sites 231
coronary arteries 180, 181 binomial system of naming 419–20, 455
albinism 369 elastic recoil 169
albumen 53 biodiversity 429–30, 455
pulmonary arteries 167, 181 decline in 440
albumin 171 arterioles 168, 170
alcoholic fermentation 259 importance of 445–7
artificial selection 394–5, 396–401 investigation of 430–6
aldoses 37–8 asexual reproduction 111, 344
alien species 451 Simpson Diversity Index 437
assisted reproduction 450–1 threats to 439–40
allele frequencies 393–4, 409, 413 asthma 193
alleles 343, 344, 357, 377 biological control 452
ATP (adenosine triphosphate) 22–3, 122, biological molecules
multiple 356 139, 241, 242–3, 265
allopatric speciation 409–10, 412 tests for 31–5, 58
generation in aerobic respiration see also carbohydrates; lipids;
all or nothing principle, action potential 245, 250, 251, 253–4
325 proteins
generation in anaerobic respiration bioremediation 479
a-helix 50 260
alveoli 194–6, 198 biosphere 440
generation in photosynthesis 278–9 biotic factors 387, 413
amino acid activation 133–4, 139 uses of 254–6 birth weight 389–90
524

biuret test 32, 33–4 carriers of recessive alleles 358–9, 473 chloroplasts 14, 15, 19, 269–70, 287
Index
bladder 303 Cas9 468 isolation of 286
blocking molecules 332 Casparian strip 145, 151, 152 light microscopy 5, 10
blood 171–3, 186 catabolic reactions 61 possible origin 26
oxygen and carbon dioxide transport catalase 66–8 thylakoid membranes 278
176–9 Catalogue of Life 429 cholera 201–4, 222
roles of 173 catalysts 62 cholesterol 47
blood clotting mechanism 473 see also enzymes in cell surface membrane 84, 103
blood glucose regulation 294–300, 315 cattle 401 chorionic villus sampling 476
blood glucose testing 299 cell–cell recognition sites 102 chromatin 15, 107
blood groups 356 cell cycle 111–13 chromatography 271–3
blood pressure 168, 197 cell division 106 chromosomes 15, 107–8, 118, 343–4,
B-lymphocytes 227–30, 228–30, 238 see also meiosis; mitosis 377
Bohr effect (Bohr shift) 178 cell-mediated immunity 227 mitosis 115–17
botanic gardens 450 cells 1, 13, 29 structure 108–10
Bowman’s capsule 302–4 comparison of animal and plant cells telomeres 110
brain 319, 341 13–14, 21 X and Y 357–8
BRCA1, BRCA2 genes 473–4 light microscopy 5–9 cilia 19
breast cancer 473–4 prokaryotic and eukaryotic 23–4 ciliated epithelium 190, 191
breathing 193 size 1–2, 28 circular chromosome 24, 25
bronchi (singular: bronchus) 189, 190–1 ultrastructure 10, 14–20 circulatory system 166–70, 186
bronchioles 190–1, 192 cell signalling 84–6, 299–300, 315 blood 171–3
Brown, Robert 3 cell surface membrane (plasma membrane) heart 179–86
bulbous head, myosin 332–4 13, 14–15, 81, 103, 418 oxygen and carbon dioxide transport
bulk transport 87, 101, 103 composition 81–2 176–9
bundles of His 184, 186 electron micrograph 83 tissue fluid and lymphatic system
by-pass vessels 174 fluidity 81–2 174–6
fluid mosaic model 83 citric acid cycle see Krebs cycle
C functions of membrane proteins 102 cladogram 405
calorimeters 246 movement of substances across 82, classes 420
Calvin cycle 280 85, 86–7 classification 420, 455
cancer 114–15, 118 see also active transport; bulk binomial system 419–20
use of monoclonal antibodies 234 transport; diffusion; osmosis kingdoms and domains 416–18
capillaries 168–70, 174 permeability 83 species 415–16
in alveoli 194–6 proteins, carbohydrates and climate change 440–1
in Bowman’s capsule 305 cholesterol 84 Clinistix™ 77–8, 299–300
forces for exchange 175 signalling functions 84–6 clonal selection 228
thermoregulation 294–5 water movement across 98 Clostridium difficile 218, 220
capsid 26, 27 cell theory 3–4 Clostridium tetani 261
captive breeding programmes 448–9, 455 cellulose 41–2 coding strand, DNA 130
carbaminohaemoglobin 179 digestion of 401 codominance 355, 357, 377
carbohydrates 36, 58 cell wall 13, 20, 24, 25 codons 130, 135, 137, 139
in cell surface membrane 84, 103 censuses 430 coenzyme A (CoA) 242–5, 251
disaccharides 38–9 central nervous system 319 cohesion, water 154–5
monosaccharides 36–8 central tendency 389 cohesion–tension theory 154–5
polysaccharides 39–42 centrioles 19, 116 collagen 53
testing for sugars 31–2, 34–5 centromere 107, 108, 116, 343, 344 collecting ducts 303, 304, 308, 311
carbon 36 centrosome 14, 19, 117 collenchyma 147, 148
organic and inorganic 271 CFTR protein 474 colorimeters 68–9, 78
carbon dioxide, diffusion in alveoli 196 channel proteins 85, 90, 102, 474 colour-blindness 359
carbon dioxide concentration, effect on chemiosmosis 245, 253–4, 278 combustion 241
photosynthesis rate 284 chemoreceptors 322 common good 481
carbon dioxide transport 178–9 chemosynthesis 281 communication systems 317
carbonic anhydrase 172, 178 Chargaff, Erwin 124 see also endocrine system; nervous
carbon monoxide poisoning 178 chiasmata (singular: chiasma) 345, 347 system
carboxyl group 48 chi-squared (c2) test 365–7 communities 429
carcinogens 114–15, 118 Chlamydomonas 2, 421 companion cells 147, 160–1
cardiac cycle 182–3, 186 chloride shift 178–9 comparative serology 404–5
cardiac muscle 180 chlorophyll 287 compensation point 283
cardiac output 184 absorption and action spectra 274 competition 386–9, 429, 442
carnivores 427 chromatography 271–3 competitive exclusion principle 442
carotenoids 272–3 structure 273 competitive inhibition 74–5
525

complementary base pairing 123, 135, influencing factors 87 role in water transport 151, 152
Index
226 and surface area: volume ratio 88–9 endoplasmic reticulum 15, 16
complementary DNA 460 digestive enzymes, effect of pH 71–2 endosymbiotic theory 26
complement proteins 224–5 digital microscopy 6 endothelium 169, 170
compound light microscope 4–9 dihybrid cross 360–3, 377 energy 240
condensation reactions 38, 54, 121, 122 Drosophila (fruit fly) 363–5 uses of 241–2
conservation 455 diploid (2n) state 110, 344, 357, 377 energy currency 242
alien and invasive species 451–3 dipoles 40, 55 energy stores
assisted reproduction 450–1 directional selection 390 fats and oils 45, 246
captive breeding programmes 448–9 disaccharides 38–9 starch 287
nature reserves 447–8 discontinuous variation 380–1 energy value of nutrients 245–6
role of non-governmental disease 200–1, 222 environment
organisations 453–4 see also genetic disorders; infectious effect on phenotype 356, 367, 380,
seed banks 449–50 diseases 383
conservative DNA replication 126 disruptive selection 391 impact on population size 389
continuous variation 380–1 distal convoluted tubule 304, 308 enzyme-catalysed reactions 66–7, 78–9
contractile vacuole 97 disturbing factors 394–5, 413 effect of enzyme concentration 73
Convention on International Trade in disulfide bonds 51 effect of pH 71–2
Endangered Species (CITES) 454 DNA (deoxyribonucleic acid) 107, 118, effect of substrate concentration
convoluted tubules 302, 303, 305–7 120–1 72–3
coral reefs 440–1 comparison with RNA 128 effect of temperature 70–1
coronary arteries 180, 181 mutations 114 measuring the rate of reaction 67–8
correlation 435–7 packaging in chromosomes 108–10 Michaelis–Menten constant (Km)
cotransporter proteins 85 replication 125–8 73–4
counter-current multiplier mechanism structure 123–4 using a colorimeter 68–9
307–8 studies of relatedness 406–7 enzymes 51, 78, 102
Crick, Francis 124 triplet codes 129–31, 135 active sites 64
CRISPR (Clustered Regularly Interspaced DNA electrophoresis 468–9 effect on activation energy 63–4
Short Palindromic Repeats) 468 DNA ligase 459 extracellular and intracellular 62
cristae 17 DNA microarrays 470, 471 immobilised 76–8
crossing over 345, 347, 348–9 DNA polymerase 125, 126–7, 459, 460 induced fit hypothesis 65–6
cyclic AMP (cAMP) 297, 315 DNA sequencing 459, 485 inducible and repressible 375
cyclic photophosphorylation 279 DNA viruses 26, 426 industrial uses 76
cystic fibrosis 474–5 dodo 444–5 inhibitors of 74–5
gene therapy 478 domains 417–18 lock-and-key hypothesis 64
cytokinesis 110, 113, 116 domestication 397 mode of action 62–6
cytoplasm 13 dominant alleles 352, 357, 368, 377, 473 names of 66
cytosine 121 Huntington’s disease 371–2 role in metabolism 61–2
double circulation 166–7, 168, 186 specificity 65
D Drosera rotundiflora 336 use in genetic engineering 459–65,
dandelion (Taraxacum officinale) 383 Drosophila (fruit fly) 363–5 468
Darwin, Charles 396–7, 402, 410–11 drug development 446 epidermis, plants 144, 147
databases 471 Escherichia coli 2, 23–4
DDT 205 E genetic engineering 459–65
deamination 301 ecological separation 410 ethics 447, 480–1, 484–5
decomposers 427 ecosystems 426–7, 440 Eukaryota 417–18, 420
deforestation 445, 447 biodiversity 430 eukaryotic cells 23, 24, 29
degrees of freedom 366 ecotourism 446 genetic engineering 466
DELLA proteins 376–7 edge effects 448 evaporation 56
demes 412 effectors 317, 341 evolution 402–3, 413
denaturation of protein 53 electrocardiography (ECG) 185–6 hominids 443
by heat 71 electron carrier proteins 102 molecular evidence 403–7
dendrons and dendrites 320 electron microscopy 10–12, 29 excitatory synapses 326–8
deoxyribose 38 cell structure 14 excretion 302, 315
detrivores 427 electron transport chain 252–3 exocrine glands 318
diabetes 300 electrophoresis 468–9, 485 exocytosis 101
insulin production 459–66, 472 elephants, endangered status 443–4 exons 132
diaphragm 189, 193 emulsion test 32, 33 expiration 193
diastole 182, 183 endangered species 443–4, 454 expression vectors 464
diffusion 87–8, 103, 142 endemic diseases 200 extinctions
in cells 89–90 endocrine system 296, 315, 318–19 driving forces 440–5
facilitated 90 endocytosis 101 mass extinction events 441
gas exchange 188, 196 endodermis 145 extremophiles 417, 459, 461
526

F genetic disorders 473–4, 485 H
Index
albinism 369
facilitated diffusion 85, 90 habitat loss 444, 445, 447, 455
cystic fibrosis 474–5
factor VIII production 472 habitats 428
haemophilia 371
FAD (flavine adenine dinucleotide) 244, biodiversity 430
Huntington’s disease 371–2
245 haemoglobin 52, 172, 177–8, 186
sickle cell anaemia 52, 355, 369–71
families 420 comparisons between species 404
genetic drift 394
fats see triglycerides HBB gene mutation 369–71
genetic engineering 399, 458–9, 485
fatty acids 43, 44 haemophilia 371, 459–66
in agriculture 482–5
fermentation 259–60 haploid (n) state 110, 344, 357
benefits and hazards 479
ferns 423 Hardy–Weinberg principle 393–4
ethical issues 480–1
fertilisation 344 Heaf test 209
in eukaryotes 466
fibres 143, 146 health 200, 222
insulin production 459–66, 472
fibrin 51 heart 180, 181, 186
markers 464, 466, 467
fibrous proteins 51, 53, 58 cardiac cycle 182–3
social implications 480
flaccidity 94 electrocardiography 185–6
genetic fingerprinting 459, 468, 485
flagella 19, 24, 25 heart beat, origin and control of
genetics 377
flowering plants 423 184–5
dihybrid cross 360–5
fluid mosaic model 83, 103 heart block 185–6
of gibberelin formation 372–3
fluorescent markers 466, 467 heart rate 184–5
monohybrid cross 350–6
food crops 398 heart valves 180–2
pedigree charts 368
genetic engineering 399, 483–4 heat production 256, 294
population genetics 392–6
rice 261–3 heavy metal tolerance 408
probability and chance 365–7
selective breeding 399–400 hemicelluloses 42
sex chromosomes 357–8
food shortages 482 herbicide-resistant crops 483–4
sex linkage 358–9
fossil record 415 herbivores 427
genetic screening 475–6
founder effect 395 herd immunity 237
ethical issues 481
Franklin, Rosalind 124 heterotrophic nutrition 240
genetic technology 485
Fucus 421 heterozygous 350, 357, 377
see also DNA sequencing; genetic
functional groups 37 Hill reaction 285–6
engineering
Fungi 416, 422, 455 histone 108–9
genetic variation 348–9, 380–1, 430,
HIV/AIDS 212–15, 222
445–6
G genotype 350, 357
homeostasis 291–2, 315
Galapagos islands 410–11 blood glucose regulation 294–7
geographic isolation 409–10, 448
gametes 344 in the kidneys 301–11
germination 340
gas exchange 188, 198 negative feedback 293
gibberelins (GAs) 337, 338, 340,
alveoli 194–6 in plants 312–14
372–3
respiratory system 188–92 hominid evolution 443
gene activation 376–7
ventilation of the lungs 193 homologous pairs of chromosomes 344,
globular proteins 51, 52, 58, 84, 103
water loss 192 345
enzymes 61–2
gated channels 324 homozygous 350, 357, 377
glomerulus 302, 304
gene editing 467–8 honey bee (Apis mellifera) 367, 383
glucagon 296, 297, 318
gene isolation methods 466–7 Hooke, Robert 3
glucose
gene mutations 137–8, 139 hormones 318–19, 341
a- and β- forms 37
gene pools 392–3, 413, 428 see also antidiuretic hormone; insulin;
structure 36–7
changes in 409 thyroxin
see also blood glucose regulation
disturbing factors 394–5 Human Genome Project (HGP) 467
glucose measurements 301
gene probes 469 human rights 481
glyceraldehyde 38
genera (singular: genus) 420 humoral immunity 228
glycerol 43, 44
gene regulation 374–7 hunting by humans 443–5
glycogen 14, 41
genes 129, 343, 357 Huntington’s disease 371–2, 473
glycolipids 84
gene splicing 462 hybridoma cells 233
glycolysis 245, 249, 250, 257, 265
gene therapy 477–9, 485 hydrogen bonds 39–40, 51, 90–1
glycoproteins 84, 225–6
genetically modified (GM) organisms in water 55, 154
glycosidic bonds 38, 54
458, 482, 485 hydrolysis reactions 39, 54
glyphosate-resistant crops 483
ethical issues 484–5 hydrophilic molecules 52, 55, 57, 154
goblet cells 190, 191
herbicide-resistant crops 483–4 hydrophobic molecules 43
Golgi apparatus 15, 17, 101
insect-resistant crops 484 hyperglycaemia 294
grana (singular: granum) 19, 269
salmon 482 hypertonic solutions 94
graticules 8
genetic bottlenecks 394, 395 hyphae 422
grey squirrel (Sciurus carolinensis) 451–2
genetic code 129–31, 135, 139 hypoglycaemia 294
growth movements 335–6
genetic counselling 477, 485 hypothalamus 308–9, 318
guanine 121
genetic dictionary 131, 135, 137 hypotonic solutions 94
guard cells 153, 312–14
527

I kidneys 301–3, 315 M
Index
urine formation 302–11

immobilised enzymes 76–8 macromolecules 53–4
kingdoms 415, 416, 420, 421–4,
immune system 225, 227–30, 238 see also nucleic acids;
455
recognition of ‘self’ 225–7 polysaccharides; proteins
evolutionary relationships 425
immunity macrophages 101, 194, 195, 225, 226
Krebs cycle 249, 251–2, 265
comparative serology 404–5 antigen presentation 228, 229
herd immunity 237 magnesium deficiency, plants 160
types of 236 L magnification 9
inbreeding depression 399, 446 Lack, David 410–11 maize, selective breeding 399–400
independent assortment 348, 349, 361–2 lac operon (lactose operon) 375, 464 major histocompatibility complex (MHC)
indoleacetic acid (IAA) 337, 338, 341 lacteals 175 antigens 226
induced fit hypothesis of enzyme action lactate fermentation 259–61 major mineral elements 158
65–6 lactose 39 malaria 200, 205–7, 222
Industrial Revolution 440 lagging strand, DNA replication 126 and sickle cell trait 391–2
infection Law of Independent Assortment 362 malignant tumours 114
immune response 225–30 Law of Segregation 352 maltose 39
non-specific responses to 224–5 leading strand, DNA replication 126 mark, release and recapture (MRR)
infectious diseases 200–1, 222 leaves, structure 144 technique (Lincoln Index) 433, 435,
cholera 201–4 ligands 84 436
HIV/AIDS 212–15 ligase 462 Marran grass (Ammophila) 158
malaria 205–7 light, as an energy source 271 mass flow 151, 152, 161, 164
tuberculosis (TB) 208–11 light-dependent stage of photosynthesis mass flow hypothesis 162–3
influenza (flu) 201 275–9 mean 389
inheritance see genetics light-independent stage of photosynthesis median 389
inhibitors 74–5 280 meiosis 110, 111, 344–8, 377
inhibitory synapses 329 light intensity, effect on photosynthesis genetic variation 348–9
inspiration 193 rate 283–4 melanin 382
insulin 295–6, 318 light microscopy 4–9, 29 memory cells 230
production of 459–66, 472 lignin 146 Mendel, Gregor 351
treatment of diabetes 299 Lincoln Index (MMR technique) 433, 435, mesophyll cells 144
interferons 224–5 436 mesophytes 156
intermediate neurones 319–20 line transects 433 messenger RNA (mRNA) 128, 131–3, 139
internal transport systems link reaction 249, 251, 265 genetic dictionary 137
mammals 166–85 Linnaeus, Karl 415 isolation of 460
plants 142–74 lipids 42, 58 post-transcriptional modification
International Union for the Conservation in cell surface membrane 103 132, 134
of Nature (IUCN) 453–4 emulsion test 32, 33 metabolic water 45, 253
interphase 112, 118 phospholipids 46 metabolism 61–2, 78
DNA replication 125–8 respiration of 245–7 metaphase
interspecific competition 429 steroids 46–7 meiosis 346, 347, 348
intraspecific competition 429 triglycerides 43–6 mitosis 116, 117
introns 132 waxes 47 metastasis 114
invasive species 451–3 liposomes 477, 478 Michaelis–Menten constant (Km) 73–4,
in-vitro fertilisation (IVF) 450–1 loci 344 78
ion channels 324 lock-and-key hypothesis of enzyme action microarrays 470, 471
ionic bonds 51 64 microhabitats 427, 428
ion regulation 308 locus 343, 357 microscopy 4, 29
ion uptake, plants 150, 158 loops of Henle 302, 303, 306–7 arteries and veins 169–70
iron bacteria 281 lungs 189, 198 blood components 173
irreversible inhibitors 75 air composition 196 calculating magnification and real
islets of Langerhans 295 alveolar structure and gas exchange size 6–8
isotonic solutions 94 194–6 electron microscopes 10–12
bronchi and bronchioles 190–2 light microscopes 4–9
J lymphatic system 174–6, 186 magnification and resolution 9
lymph nodes 175, 176 measuring objects 8–9
Japanese knotweed (Fallopia japonica)
lymphocytes 172, 225, 227–30, plant cells 147–8
452–3
238 recording observations 6
justice 481
T-lymphocytes and AIDS units of length 2
212–13 microtubules 19
K lysosomes 15, 17, 18 microvilli 19
keratin 51 lysozyme 51 Mimosa pudica 336
ketoses 37–8 mineral deficiencies, plants 159
528

minerals uptake, plants 150, 158 niches 427–8 pepsin, effect of pH 72
Index
mitochondria 15, 17, 254, 257 nitrate deficiency, plants 159 peptide bonds 49, 54
possible origin 26 nitrifying bacteria 281 pericardium 180
mitochondrial DNA (mDNA) 406–7 nitrogen fixation, Azolla 263 peripheral nervous system 319
mitosis 110, 111, 112–13, 118 nitrogenous bases 121, 139 peripheral proteins 84
chromosome behaviour 115–17 complementary base pairing 123 pH
significance of 110–11 nodes of Ranvier 320 denaturation of protein 53
MMR vaccine 237 non-competitive inhibition 74–5 effect on enzyme-catalysed reactions
mode 389 non-cyclic photophosphorylation 278–9 71–2
molecular clock 404–6 non-infectious diseases 200, 222 regulation of 308
monoclonal antibodies 232–3, 238 non-reducing sugars, testing for 32, 35 phagocytes 172, 225, 226, 228
production of 233 non-vertebrates 424 phagocytosis 101
uses 234–5 noradrenaline 326 phenotype 350, 357
monohybrid cross 350–4, 377 nuclear division 110 effect of environment 367, 380, 383
modification of 3 : 1 ratio 355–6 see also meiosis; mitosis effect of mutations 138
monomers 53–4 nuclear envelope 15 phloem 143, 164
monosaccharides 36–8, 58 nucleic acids 54, 118, 120–1, 139 structure 147, 160
functional groups 37 direction in 122 transport function 161–3
mosquito, malaria transmission 205–6 see also DNA; RNA phospholipids 46, 58, 81, 82, 103, 418
mosses 423 nucleolus 15 photophosphorylation 278–9
motor neurones 319–20 nucleotides 121–2, 243–4 photosynthesis 240, 281, 285, 287
MRSA (methicillin-resistant Staphylococcus condensation reactions 122–3 energy transfer 270–1
aureus) 218, 219 nucleus 13, 15–16, 106–7, 118 Hill reaction 285–6
multiple alleles 356, 377 electron microscopy 12 light-dependent stage 275–9
multipotent cells 113 light microscopy 5 light-independent reactions 280
muscle contraction 255–6, 329–31, null hypothesis 384 path of carbon 281
332–4 photosynthesis rate
mutagens 138 O limiting factors 283–5
mutations 114, 118, 137–8, 139, 356, oedema 176 measurement 282
395, 485 oils see triglycerides photosystems 276–7, 278
HBB gene 369–70 open circulation 167 phylums 420
TYR gene 369 orders 420 pili 24, 25
Mycobacterium tuberculosis 208 organelles 13, 14–20, 29 pinocytosis 101
myelin 46, 320 organic compounds 36 pituitary gland 308–9, 318
myofibrils 330, 331 osmometers 92 plankton, population fluctuations 387
myogenic origin of heartbeat 184 osmoregulation 97, 308–11, 315 Plantae 416, 423, 455
myosin 255, 331, 332–4 osmosis 87, 90–3, 103 plant cells 13–14, 21
myxomatosis 388, 452 in animals 96–7 cytokinesis 113
in plants 93–6 microscopy 147–8
N ovaries 318 osmosis 93–6
NAD (nicotinamide adenine dinucleotide) oxidative phosphorylation 252–3 plant growth regulators 336–40, 341
243, 244 oxygen diffusion, alveoli 196 plants
NADP (nicotinamide adenine dinucleotide oxygen dissociation curve 177 homeostasis 312–14
phosphate) 275, 276 Bohr effect 178 internal transport 142–52
natural immunity 228–30, 236 oxygen transport 176–9, 186 mineral deficiencies 159
natural selection 389–92, 394, 413 oxyhaemoglobin 177–8, 186 photosynthesis 270–1, 275–81
nature reserves 447–8, 455 translocation 160–3
transpiration 153–6
negative correlation 435 P plant sensitivity 341
negative feedback 293, 311, 315 pacemaker 184, 186
Neo-Darwinism 402–3 control and co-ordination 335–6
pancreas 296, 318 plasma 171, 173
nephrons 302–3 pandemic diseases 201
nerve impulses 333-6 plasma cells 228, 229
Paramecium 421, 442 plasma membrane see cell surface
sodium–potassium pumps 100 parenchyma 147, 148
nervous system 296, 315, 319–20, 341 membrane
partially permeable membranes 91, 103 plasmids 462, 463–4, 465, 483, 485
reflex arcs 321 partial pressures 177
sense organs 321–2 plasmodesmata (singular: plasmodesma)
passive immunity 236 20, 161
synapses 326–9 Pasteur, Louis 3
transmission of an impulse 323–6 Plasmodium 205
pathogens 200 plasmolysis 94, 95–6
neuromuscular junctions (motor end Pearson’s linear correlation 436–7
plates) 331–2 platelets 172, 173, 473
pectins 42 podocytes 304
neurones 319–20, 341 pedigree charts 368
neutrophils 225, 226 polar molecules 55
pentose sugars 121
529

polygenic inheritance, polygenes 381–2 purines 121 restriction endonuclease 459, 462, 463,
Index
polymerase chain reaction (PCR) 461 Purkyne tissue 184, 186 465, 468, 485
polypeptides 49, 58 pyrimidines 121 retroviruses 213
polysaccharides 39–42, 58 pyruvate production reverse transcriptase 459, 460, 485
see also cellulose; glycogen; starch aerobic respiration 259 R-group 37, 48
polysomes 135 anaerobic respiration 259 ribose 38
polyunsaturated fats 44 ribosomes 15, 16, 17, 18, 139
population fluctuations 387, 388 Q location in cells 135
population genetics 392–6 quadrats 431–2 protein synthesis 132, 134, 136
population growth 202, 440, 455 quaternary structure of a protein 50, rice (Oryza sativa) 261–2
populations 392, 413, 428 58, 231 RNA (ribonucleic acid) 120–1, 128
isolation of 409–12 see also messenger RNA; transfer RNA
population size 446 RNA polymerase 131–2
pores, cell surface membrane 83, 90
R RNA splicing 132
positive correlation 435 rabbits, introduction to Australia 387–8, RNA viruses 26, 426
post-transcriptional modification 132 452 root hairs 149–50
potometers 155–6 rainforests 445, 447 uptake of ions 158
pre-capillary sphincters 174 random sampling 430–2 roots, structure 145
pregnancy testing 234–5 receptors 84–5, 102, 317, 321–2, 341 rough endoplasmic reticulum (RER)
prenatal screening 476 recessive alleles 352, 357, 368, 377, 473 15, 16
pressure flow hypothesis 162–3 carriers 358–9 R-plasmids 464, 465, 485
pressure potential 93 TYR gene mutations 369 rubisco (ribulose biphosphate
prey–predator population oscillation recombinant DNA 458 carboxylase) 280
388 recombinant DNA technology see genetic
primary structure of a protein 49, 51, engineering S
58, 231 recombinant human proteins 472–3
recombinants 348, 360 salmon, genetic modification 482
probability, chi-squared (c2) test 365–7 saltatory conduction 326
producers 427 red blood cells (erythrocytes) 12, 52,
171–2, 173, 186 sand dunes 438
profile transects 432, 434 sarcolemma 180
Prokaryota 416, 455 red–green colour blindness 359
redox indicators 258 sarcomeres 331
prokaryotic cells 23–4, 29 sarcoplasmic reticulum 329, 330
promotor genes 375, 464, 485 redox reactions 243
reducing sugars 38, 58 saturated fats 43–5
prophase scanning electron microscopes 12
meiosis 345–6, 348 testing for 31–2, 34–5
reflex arcs 321 Schleiden, Matthias 3
mitosis 116, 117 Schwann, Theodor 3
proteins 48, 58 refractory period
cardiac muscle 184 Schwann cells 320
amino acids 48 secondary structure of a protein 50, 51,
in blood 171 neurones 325
regulators 291–2 58, 231
in cell surface membrane 84–6, 90, seed banks 449–50
102, 103 regulatory genes 356, 374
replication forks 125 selective breeding 394–5, 396–401
denaturation 53, 71 selective predation 394
globular and fibrous 51–3 resolution 9
respiration 188, 240–1, 265 ‘self’, recognition of 225–7
interactions within a polypeptide 51 semi-conservative DNA replication
peptide bonds 49 aerobic 249–57
anaerobic 259–61 126–8
respiration of 245–7 semilunar valves 181
roles of 54 electron transport chain 252–3
energy transfer and ATP synthesis sense organs 321–2
structure 49–51, 231 sensory neurones 319–20
testing for 32, 33–4 245, 253–4
Krebs cycle 251–2 septum of the heart 180
protein sequence data 403 severe combined immunodeficiency (SCID)
protein synthesis 139, 255 location of 257
nucleotides involved in 242–5 472–3
amino acid activation 133–4 sex chromosomes 357–8, 377
DNA triplet codes 129–31 redox reactions 243
use of lipids and proteins 245–6 sex determination 358
genetic control 375–6 sex linkage 358–9
transcription 131–3 respiration rate, influencing factors 258
effect of temperature 263–5 haemophilia 371
translation 134, 136 sexual reproduction 344, 350
proteome 458 respiratory intermediates 258
respiratory pigments 189 sickle cell anaemia 52, 355, 369–71
Protoctista 416, 421, 455 sickle cell trait 206, 207, 391–2
proto-oncogenes 114 see also haemoglobin
respiratory quotient (RQ) 246–7, 265 sieve plate 160–1
proximal convoluted tubule 303, 305 sieve tubes 147, 160–1, 162
pulmonary circulation 167, 168, 186, 194 respiratory surfaces 189
respiratory system 188–96 Simpson Diversity Index 437
pulse 184 single circulation 167
pump proteins 99–100, 102, 158 respirometers 264–5
resting potential 323 sink area 161
Punnett squares 353
530

sinoatrial node (SA node, pacemaker) systemic circulation 167–8, 186 transport mechanisms see active
Index
184, 186 systole 182–3 transport; bulk transport; diffusion;
size relationships 27–8 internal transport systems; osmosis
skeletal muscle see striated muscle T tricuspid valve 181
skin tachycardia 185–6 triglycerides 43, 58
colour of 382 Taq polymerase 461 formation of 44
sliding-filament hypothesis, muscle target organs 318 roles in living things 45–6
contraction 333–4 taste buds 322 saturated and unsaturated 43–5
smooth endoplasmic reticulum (SER) 15, taxonomy 419 triplet codes 129–31, 135, 139
16 see also classification tropomyosin 332
sodium–potassium pumps 100 telomeres 110 trypsin, effect of pH 72
solute potential 92 telophase t-test 383–5
somatic gene therapy 477, 478 meiosis 346, 347, 348 tuberculosis (TB) 208–11, 222
Sorghum 157 mitosis 116, 117 tumours 114, 118
source area 161 temperature tumour-suppressing genes 114
Spearman’s rank correlation 436–7 denaturation of protein 53 turgidity 93, 94, 96
speciation 394–5, 409–12 effect on enzyme-catalysed reactions TYR gene 369
species 407–8, 415–16, 420, 455 70–1
biodiversity 429–30 effect on photosynthesis rate U
Species 2000 programme 429 284 ultrafiltration 304–5
sphygmomanometer 197 effect on respiration rate 263–5 unicellular organisms 1, 2
spinal cord 319 temperature coefficient 71 unipotent cells 113
spindle 116 tertiary structure of a protein 50, 51, unsaturated fats 43–5
stabilising selection 389–90 58, 231 uracil 121
stability of community 439 test crosses 357 urea 302
stage micrometers 9 dihybrid 362–3 ureters 302
starch 14, 40 monohybrid 354 urethra 302
enzyme-catalysed hydrolysis 70 testes 318 urinary system 303
testing for 32, 33 testis determining factor (TDF) 358 urine formation 302–10
statistical software 437–9 tetanus 261 utilitarianism 481
statistical tests 383–5 T-helper cells 228, 229
chi-squared (c2) test 365–7
for correlation 435–7
T-killer cells 227 V
threshold of stimulation 325 vaccination 236–7, 238
stele 145 thylakoid membranes 19, 269,
stem cells 113 BCG (Bacillus Calmette–Guérin)
278, 287 209–10
stem of plants 143 thymine 121
steroids 46–7 vacuoles 15
thymus gland 227, 318 contractile 97
stimuli 317 thyroid gland 318
stomata 144, 153 permanent 20
Ti plasmid 483 valves
regulation of 312–14, 315 tissue fluid 174, 186
Streptococcus pyogenes 12 of the heart 180–2
T-lymphocytes 212–13, 227, 238 in veins 169
striated muscle tobacco mosaic virus 27
contraction 332–4 van der Waals forces 51
tonoplast 20 van Leeuwenhoek, Anthony 3
structure 329–31 trachea 189, 190, 191
stroke volume 184 variation 380–2, 413
tracheids 146 see also genetic variation
structural genes 374 transcription 131–3, 139
subcutaneous fat 46 varieties (sub-species) 408
genetic control 376 vasa recta 303, 306–7
suberin 145 transects 432–3, 434
substrates 64 vascular bundles 143–4
transfer cells 162 veins 168–70
concentration, effect on enzyme- transfer RNA (tRNA) 128, 133–4, 139
catalysed reactions 72–3 valves 169
transformed bacteria 463–4 vena cava 167, 168, 181
sucrose 38–9 transgenic organisms 458
translocation 161–3 ventilation mechanisms 189
see also genetic engineering ventricles 180, 181, 186
sugars translation 134, 136, 139
disaccharides 38–9 ventricular fibrillation 185–6
translocation 160–3 ventricular systole 182, 183
monosaccharides 36–8 transmission electron microscopes
surface area: volume ratio 88–9, venules 168, 170
10–12, 29 Venus fly trap (Dionaea muscipula)
188–9 transmitter substances 326–8, 331
surfactant cells 194, 195 338
transpiration 153–5, 164 vertebrates 424
sympatric speciation 410–12 influencing factors 156
symplast pathway 151, 152 vesicles 101
role of 156 Vibrio cholerae 202
synapses 326–9, 341 transpiration stream 152, 154
neuromuscular junctions 331–2 Virchow, Rudolf 3
531

virtue 481 water balance 192 Y
Index
viruses 26–7, 29, 222, 425–6 water potential 91–2, 103, 150
Y chromosome 357, 377
use in gene therapy 477, 479 and animal cells 97
yeasts 422
of plant tissue 94–5, 96
genetic engineering 466
W Watson, James 124
waxy cuticle, leaves 144
water 31, 58
white blood cells (leucocytes) 172, 173, Z
conservation in kidney 306–8
186 Z lines 331
evaporation and heat loss 56
Wilkins, Maurice 124 zoos 448–9
hydrogen bonds 55, 56, 154
wilting 96 zygote 344
metabolic 45, 253
molecular structure 39–40, 55, 56
movement across the cell surface X
membrane 98 X chromosome 357, 377
movement through a plant 149 xerophytes 157–8
see also transpiration xylem 143, 164
in plasma 171 structure 146
solvent properties 56–7 transpiration stream 154–5
specific heat capacity 55–6 water transport 149, 152
summary of properties 57
uptake by root hairs 150
532

Acknowledgements
Acknowledgements
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Library; bl © Eye Of Science/Science Photo Library, br © Power b © C J Clegg; p.269 © Dr Kenneth r. Miller/Science Photo
and Syred/Science Photo Library; p.16 t © Medimage/Science Library; p.292 tl © Silver – Fotolia, tm © Michaklootwijk/stock.
Photo Library, b © Omikron/Photo Researchers, Inc./Science adobe.com, tr © Janthonjackson – Fotolia, ml Jan-Dirk Hansen –
Photo Library; p.17 t © Carolina Biological Supply, Co/Visuals Fotolia, bl © Juniors Bildarchiv GmbH/Alamy Stock Photo; p.293
Unlimited, Inc./Science Photo Library, b © CNRI/Science Photo © Nickel ElectroLtd; p.295 © Astrid & Hanns-Frieder Michler/
Library; p.19 © t Don W. Fawcett/Science Photo Library, b © Dr Science Photo Library; p.299 © dalaprod – Fotolia; p.300 t ©
Kari Lounatmaa/Science Photo Library/Getty Images; p.20 © Dr Cordelia Molloy/Science Photo Library, b © Garo/Phanie/Rex
Jeremy Burgess/Science Photo Library; p.21 l © J.C. REVY, ISM/ Features; p.303 © age footstock/SuperStock; p.304 © Steve
SCIENCE PHOTO LIBRARY, r © Gene Cox; p.24 © Kwangshin Kim/ Gschmeissner/Science Photo Library/Getty Images; p.327 ©
Science Photo Library; p.27 tl © A. Dowsett, Health Protection Prof S. Cinti/Science Photo Library; p.330 t © Gene Cox, b ©
Agency/Science Photo Library, bl © Nigel Cattlin/Alamy Stock Mediscan, University of Aberdeen; p.331 © Mark Rothery, A
Photo, br © Nigel Cattlin/Alamy Stock Photo; p.32 both © Level Biology, www.mrothery.co.uk; p.333 © Mark Rothery, A
Andrew Lambert Photography/Science Photo Library; p.33 t Level Biology, www.mrothery.co.uk; p.336 l © Martin Shields/
both © Andrew Lambert Photography/Science Photo Library; Alamy Stock Photo, r © FLPA/Alamy Stock Photo; p.338 ©
b © Trevor Clifford Photography/Science Photo Library; p.41 Ernie Janes/Alamy Stock Photo; p.345 © Science VU/B. John,
© Dennis Kunkel Microscopy/Science Photo Library, p.42 © Visuals Unlimited /Science Photo Library; p.351 © Chronicle/
Biophoto Associates/Science Photo Library; p.43 tl © Uckyo/ Alamy Stock Photo; p.359 © Sally and Richard Greenhill/Alamy
stock.adobe.com, tm © quayside – Fotolia, tr © Profotokris Stock Photo; p.364 © Denis Crawford/Alamy Stock Photo; p.367
– Fotolia; p.46 © Steve Gschmeissner/Science Photo Library/ l © Frank Greenaway/Dorling Kindersley/Getty Images, m ©
Alamy Stock Photo; p.53 © Steve Gschmeissner/Science Photo alexfiodorov – Fotolia, r © Frank Greenaway/Dorling Kindersley/
Library; p.69 © Martyn F. Chillmaid/Science Photo Library; Getty Images; p.369 © Friedrich Stark/Alamy Stock Photo;
p.78 © Cordelia Molloy/Science Photo Library; p.83 both © p.378 © New Africa/stock.adobe.com; p.383 l © Gene Cox, m ©
Don W. Fawcett/Science Photo Library; p.96 both © Biophoto tina7si – Fotolia, r © Martin Fowler/Alamy Stock Photo; p.388
Associates/Science Photo Library; p.109 © Biophoto Associates/ l © Mitsuaki Iwago/Minden Pictures/SuperStock, r © Adrian
Science Photo Library; p.116 all © Michael Abbey/Science Photo Sherratt /Alamy Stock Photo; p.391 © Greenwales/Alamy Stock
Library; p.124 l © A. Barrington Brown, © Gonville & Caius Photo; p.395 both © CJ Clegg; p.397 l © Dave Watts/Alamy
College / Science Photo Library, m © Science Photo Library, r Stock Photo, m © Kerryhilden/Shutterstock.com, r © Nigel
© Science Photo Library; p.143 l © Ed Reschke/Peter Arnold/ Cattlin / Alamy Stock Photo; p.400 l © EcoView/stock.adobe.
Getty Imagesboth, r © Dr Keith Wheeler/Science Photo Library; com, m © Inga spence/Alamy Stock Photo, r © Tanguy LeNeel
p.144 © Gene Cox ; p.145 both © Gene Cox; p.146 © Gene Cox; / Alamy Stock Photo; p.401 © wolfavni – Fotolia; p.410 © “©
p.147 © Gene Cox; p.150 both © Gene Cox; p.153 © Gene Cox; Morley Read/Alamy Stock Photo; p.411 l © Jack Stein Grove/
p.155 t © Biophoto Associates/Science Photo Library, b © Dr Danita Delimont, Agent/Alamy Stock Photo, r © Wayne Lynch/
David Furness, Keele University/Science Photo Library; p.158 © All Canada Photos/Alamy Stock Photo; p.418 r © CJ Clegg;
Gene Cox; p.161 © Biophoto Associates/Science Photo Library; p.419 l © Idp wildlife collection/Alamy Stock Photo, m © Lip
p.169 © CNRI/Science Photo Library; p.172 © Gene Cox; p.180 Kee / http://www.flickr.com/photos/lipkee/5657636385/sizes/o/
© Gene Cox; p.185 © Ivan Taborau/Alamy Stock Photo; p.190 © in , r © FLPA/Alamy Stock Photo; p.420 l © Alta Oosthuizen/
Steve Gschmeissner/Science Photo Library; p.191 t © Dr Gladden stock.adobe.com, m © DDniki – Fotolia, r © Picture.jacker/
Willis, Visuals Unlimited/Science Photo Library, b © Biophoto stock.adobe.com; p.421 t © Power And Syred/Science Photo
Associates/Science Photo Library; p.192 t © Science VU/Visuals Library, b © Dr David Patterson/Science Photo Library; p.422
Unlimited, Inc./Science Photo Library, b © Alaska Stock LLC/ tl © Mediscan/Alamy Stock Photo, ml © Sabena Jane Blackbird/
Design Pics Inc/Alamy Stock Photo; p.193 © Andrzej Tokarski – Alamy Stock Photo, mr © Antony Ratcliffe/Alamy Stock Photo,
Fotolia; p.195 © Dr. Gladden Willis, Visuals Unlimited/Science bl © Blickwinkel/Hecker/Alamy Stock Photo, br © Blickwinkel/
Photo Library; p.196 © CMEABG/UCBL1, ISM/Science Photo Hecker/Alamy Stock Photo; p.423 t © Craig Lovell/Eagle Visions
Library; p.202 © Dr. Hans Ackermann/Visuals Unlimited, Inc./ Photography /Alamy Stock Photo, bl © David Keith Jones/
Science Photo library, p.204 t © Science & Society/SuperStock, Images of Africa Photobank/Alamy Stock Photo, bm © Bjorn
b © Paula Bronstein/Getty Images News/Getty Images; p.208 Svensson/Science Photo Library, br © Blickwinkel/Alamy Stock
t © James Cavallini/Science Photo Library, m © Adam Hart- Photo; p.428 l © Paul Heinrich/Alamy Stock Photo, r © Armin
Davis/Science Photo Library, b © Cavallini James/BSIP SA/ Staudt/stock.adobe.com; p.432 © Martyn F. Chillmaid /Science
533

Photo Library; p.433 © Paul Glendell/Alamy Stock Photo; p.438 Bryophytes and Pteridophytes, McGraw Hill, New York/London;
Acknowledgements
© CJ Clegg; p.441 l © Suzanne Long/Alamy Stock Photo, r © p.263 r, Fig 12.18; graph adapted from Moran, R.C. (1997) ‘The
Suzanne Long/Alamy; p.444 © Henk/stock.adobe.com; p.445 © little nitrogen factories’, Biological Sciences Review 10(2): 2–6,
The Natural History Museum/Alamy Stock Photo; p.449 James p.5.; p.284 Fig.13.17 adapted from T.J Blom; W.A. Straver; F.J.
King-Holmes/Alamy Stock Photo; p.451 l © John Devries/Science Ingratta; Shalin Khosla - OMAF; Wayne Brown - OMAF Carbon
Photo Library, r © protopic – Fotolia, p.452 © CJ Clegg; p.457 dioxide in greenhouses, http://www.omafra.gov.on.ca/english/
© Robin / stock.adobe.com; p.463 © Dr Gopal Murti/Science crops/facts/00-077.htm; p. 375 Fig 16.30 http://en.wikipedia.
Photo Library; p.467 tl © © Steffstarr/123 RF, br © Makoto org/wiki/Lac_operon#mediaviewer/File:Lac_Operon.svg, CC
Iwafuji/Eurelios/Science Photo Library; p.470 © Jan Van De Vel/ BY-SA 3.0; p.381 Fig 17.1 Office for National Statistics, graph
Reporters/Science Photo Library; p.473 © CNRI/Science Photo (adapted) from ‘The Heights and Weights of Adults in Great
Library; p.477 © Will & Deni Mcintyre/Science Photo Library. Britain’, (c) Crown copyright 1999, reproduced by permission;
p.389 Fig 17.8 Birth weight and infant mortality, a case of
Text credits:
stabilising selection – data from R.J. Berry (1977) The New
Artwork and data credits: Naturalist Inheritance and Natural History, HarperCollins; p.398
Fig 17.17 data from Vaughan, J. G. and Geissler, C. A. (1997)
p.159 Table 7.3 adapted from Bonner, J. and Galston, A.W. (1958) The New Oxford Book of Food Plants, Oxford University Press,
Principles of Plant Physiology, W.H. Freeman & Co., San Francisco; Oxford; p.400 Fig. 17.19 adapted from Julius Jannick (1974)
p.171 Fig 8.5 adapted from Colin Clegg (revised by S.Ingham) Plant Science: An Introduction to World Crops, W H Freeman; p.408
(1995) Exercise Physiology and Functional Anatomy; Feltham Fig 17.25 Adapted from A.D. Bradshaw and T. McNeilly (1981)
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from World Malaria Situation in 1993, Weekly Epidemiological Society, © the Biochemical Society, reproduced by kind
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S.J.G. and Denning, D.W. (1995) Tuberculosis: the global 3.29 (adapted) from Genetics and Evolution (John Murray, 1999),
challenge, Biological Sciences Review, 8; p.212 Fig 10.16 HIV/Aids reproduced by permission of John Murray (Publishers) Ltd.
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epiupdate98_en.pdf; p.214 Fig 10.20 adapted from Pantaleo, G. granted under the terms of the Open Government Licence (OGL).
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p.63 Fig 3.2 Random collision possibilities adapted from Dianne
MRSA – data from the Health Protection Agency; p.220 Fig 10.26
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Antibiotics crisis means scratch could kill, Chris Smyth (May 1,
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Variety of Life’ © Scientific American Inc. 293:3; p.471 Fig 19.11
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Microarray analysis of differential gene expression A. McLennan
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pdf/ar-threats-2013-508.pdf; p.263 t Fig 12.18 Azolla plants Every effort has been made to trace all copyright holders, but
adapted from Ingrouille, M. (1992) Diversity and Evolution of if any have been inadvertently overlooked, the Publishers will
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534

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482876_FM_Biology_i-x.indd 1 20/02/20 11:52 AM

482876_FM_Biology_i-x.indd 2 20/02/20 11:52 AM

4 Cell membranes and transport

5 The mitotic cell cycle

6 Nucleic acids and protein synthesis

482876_FM_Biology_i-x.indd 3 20/02/20 11:52 AM

9.1 The gas exchange system 188

12 Energy and respiration

15 Control and coordination

17 Selection and evolution

18 Classification, biodiversity and conservation

482876_FM_Biology_i-x.indd 4 20/02/20 11:52 AM

482876_FM_Biology_i-x.indd 5 20/02/20 11:52 AM

How to use this book

482876_FM_Biology_i-x.indd 6 20/02/20 11:52 AM

End of chapter questions

END OF CHAPTER QUESTIONS

END OF TOPIC QUESTIONS

482876_FM_Biology_i-x.indd 8 20/02/20 11:52 AM

Command word What it means

Notes for teachers

482876_FM_Biology_i-x.indd 9 20/02/20 11:52 AM

482876_FM_Biology_i-x.indd 10 20/02/20 11:52 AM

1.1 The microscope in cell studies

1.1 The microscope in cell studies

1 State the essential Cell size

482876_01_Biology_001-030.indd 1 20/02/20 12:53 PM

1 endoplasm clear ectoplasm

pseudopodia cell surface

Escherichia coli – a bacterium found in the intestines of animals, e.g. humans

482876_01_Biology_001-030.indd 2 20/02/20 12:53 PM

Hooke’s microscope, and a drawing

1.1 The microscope in cell studies

Anthony van Leeuwenhoek (1632–1723) was born

Robert Brown (1773–1858), a Scottish botanist, Leeuwenhoek’s microscope

Rudolf Virchow (1821–1902), a German pathologist,

Louis Pasteur (1822–95), a brilliant French

▲ Figure 1.2 Early steps in the development of the cell theory

482876_01_Biology_001-030.indd 3 25/02/20 1:07 PM

» the compound light microscope, using visible light;

You should bring the thing you

eyepiece lens using the

turret – as it is turned the objectives

objective lenses – ×4 (low);

fine focus – used to focus condenser – focuses light on to

▲ Figure 1.3 Light microscopy

482876_01_Biology_001-030.indd 4 25/02/20 1:11 PM

1 Observing the nucleus and cytoplasm in onion epidermis cells

1.1 The microscope in cell studies

Making a temporary mount Irrigating a temporary mount

mounted needle pipette blotting paper

▲ Figure 1.4 Preparing living cells for light microscopy

2 Observing chloroplasts in moss leaf cells

9.1 The gas exchange system 188

12 Energy and respiration

15 Control and coordination

17 Selection and evolution

18 Classification, biodiversity and conservation